I have resolved this question regarding Mystara to my own satisfaction, below is the text that will appear in the relevant section of my "Official Spelljammer timeline 2.0" when it is completed.
Mystara Timeline vs. other TSR worlds
by GMWestermeyerMystara/Spelljammer
Mystara was, for most of its existence, not part of the Advanced Dungeons & Dragons multiverse as originally described in the Player’s Handbook and Dungeon Master’s Guide. It was the setting instead for the Dungeon & Dragons game, and grew from the module X1 Isle of Dread, which sketched out the world, and was included in all of the 1980 Dungeons & Dragons: Expert Sets. In 1994 TSR converted Mystara to the Advanced Dungeons & Dragons system and subsequently made some minor attempts to add it to the multiverse setting.
In Domains of Dread the Dark Lord Meredoth is said to come from the Alphatian province of Norwold, arriving in 635 of the Barovian calendar. (p79) But Norwold was not colonized by Alphatia until 919 AC according to Dawn of the Emperors (Bk III, p7). This would put Mystara wildly out of sync with the other campaign settings, and can be discounted as an example of Ravenloft’s famous mists transferring their victims through time as well as drawing them across planes.
There are some Planescape/Mystaran cross-overs. The Planewalker's Handbook, set in 128 Ha (p53), describes the Alphatian Empire as “fallen” (p33). We know the Alphatian Empire disappeared from the surface of Mystara in 1009 AC as depicted in Wrath of the Immortals (Book II p90). The Factol's Manifesto (p 91) has the factol of the Harmonium wearing red steel armor, which was only discovered recently on Mystara.
Additionally, Uncaged: Faces of Sigil, set in 128 Ha, describes a Shadow Elf, Farrow, as an inhabitant of Sigil (p32). Farrow is spying in the Great School of Glantri when a Glantrian mage forcibly sends him to Sigil through a gate. It is unclear how long Farrow has been in Sigil, but certainly a few years. This provides a broad link between current time in Planescape and Mystara.
There is an equally vague, yet direct, link between Mystara and Spelljammer. The introductory Advanced Dungeons & Dragons boxed set First Quest includes a Spelljammer adventure in which the antagonists are heading for the Rock of Bral (AdvBk, pp. 45-54). Karameikos: Kingdom of Adventure is contemporary with First Quest (Bk3, p64) and is set in 1012 AC (this aligns with Poor Wizard’s Almanac III, also set in 1012 AC and published in 1994 like Karameikos: Kingdom of Adventure and First Quest. There is no indication that the Rock as mentioned is not contemporary with its description in SJR5 Rock of Bral, which is set in 5049 OC. This fits with the Planescape links above, as the fall of Alphatia in 1009 AC would coincide with 124 Ha.
So we have 1012 AC linked to 5049 OC, which is 1367 DR. That would make 1361 DR equal to 1006 AC.
Laterre/Mystara
There is a final TSR campaign setting that should be addressed: Earth, or at least a fantasy version of Earth. This campaign setting was not detailed in a unified series of products by TSR, but nonetheless it was detailed fairly well. The earliest details of the various Earth cultures and mythologies were in Deities & Demigods, expanded on in 2nd Edition’s Legends & Lore. Each of the major European mythological and legendary periods was further detailed in the seven book Historical Reference (HR) series. The Ravenloft line produced a setting hearkening back to its original gothic horror inspirational material with Masque of the Red Death and Other Tales and The Gothic Earth Gazetteer, each set in ‘Gothic Earth’ in the 1890s. Finally, in the Spelljammer: AD&D Adventures in Space boxed set The Concordance of Arcane Space (pp. 42 & 90) provided some very barebones detail on Solspace (including the name). Mythic/Gothic Earth did not have a single product line, but it was as well detailed across time as any of TSR’s other published settings.
In the article “Chronomancy & the Multiverse, version 1.1,” published online, Roger E. Moore explicitly linked the HR series books Mythic Earth with Gothic Earth. He went a step further, linking the Mythic/Gothic Earth with Laterre, the Earth on which the X2 Castle Amber and its sequel, Mark of Amber, placed the homeland of the d'Amberville family, Averoigne. Averoigne is one of the settings created by legendary fantasy/horror author Clark Ashton Smith.
As Rip Van Wormer has noted, this strongly implies that H.P. Lovecraft’s Cthulhu Mythos and Robert E. Howard’s Hyborean Age are both part of Laterre (aka Mythic/Gothic Earth). This connection neatly ties the Cthulhu mythos described in the 1st edition of Deities & Demigods and TSR’s Conan modules into the AD&D multiverse. Taking that thought a step further, this is likely the same magical Earth that Fafhrd and the Grey Mouser visit in the 1947 short story, “Adept’s Gambit” which Fritz Leiber retcons to their Lankhmar tales in 1968’s Swords in the Mist, which also ties TSR’s Lankhmar setting into the larger AD&D multiverse. This also provides the world from which the original Mulan of Faerun are taken. From a Spelljammer perspective it is also possible to link Laterre/Gothic Earth with the Space:1889 universe in line with the articles in Polyhedron #73 & #74.
Linking Laterre/Gothic Earth is easiest to bring into synch with Mystara, due to the d'Ambervilles, but it is complicated by that family’s penchant for sorcery and time travel. X2 Castle Amber (p19) places Averoigne in the “High Middle Ages (c.A.D. 1100 – 1350)” Mark of Amber (handout IV) places the events of X2 Castle Amber specifically in 979 AC. Roger Moore’s article places Averoigne circa A.D. 1600, and Mark of Amber (handout IV) is dated 1012 AC. Polyhedron #73 dates the discovery of Solspace by elven spelljammers to A.D. 1886 but doesn’t link it to another date, though given the elves are fleeing a goblin flotilla it implies this occurs during one of the two Unhuman Wars. The 3rd edition work, Lost Empires of Faerûn (p61), dates the snatching of Mulan slaves from Mythic Earth to -4366 DR but Powers & Pantheons (p94) specifically states they were taken from two different regions and time periods (thus explaining why the Mulan follow both the Egyptian and Babylonian pantheons).
Given these difficulties, this timeline defaults to Roger E. Moore’s explicit 1012 AC = A.D. 1600. This provides A.D. 1600 linked to 5049 OC, which is 1367 DR. That would make 1361 DR equal to A.D. 1594. However, although this link is used to let us date the Elven spelljammers’ discovery of Laterre, the nature of contacts between Laterre/Gothic Earth and the rest of the multiverse makes chronological variety not only possible but probable. Since Laterre seems to follow different physical rules than the rest of the multiverse, this makes sense.