The simple answer to this question is "no".what is the relationship between the Book of Glorious Joy and mainstream Glorantha? Are they letting you define Malkionism in Loskalm?
But it may deserve a slightly more detailed explanation than that.
When Issaries originally commissioned the work that eventually became the Book of Glorious Joy, it was intended to be the official, definitive source on Loskalm - later extended to the whole of Malkionism. As such, it was always important to make it compatible with other sources. From the beginning, it was always compatible with material that had been previously published, and I believe it still is. In addition, I had access to a number of unpublished writings from Greg's work. Once the first book was written, it was sent to Greg, he sent a number of comments back, it was revised to make sure it all fit what he wanted, some things that didn't fit were deleted, and, in general, there was discussion to make sure it was "right".
So it's not as if this is something I've just written on my own; it's not just my vision, and I have worked hard to ensure it's as canonical as it can be. However, as the fact that it was eventually published as a non-canonical source indicates, there are some fairly major caveats to that.
Firstly, the discussions with Greg over the initial manuscript were never fully completed, due to changes at Issaries, a long trip to Mexico, and so forth. At no point did he say "this is 100% correct". As a couple of examples, we never had a chance to discuss the calendar or the section on the Abiding Script at all, so these remain entirely speculative (and, especially in the former case, likely quite different from the eventual canon).
A second point to be made is that, since all this happened several years ago, he may well have changed his mind since, as is his prerogative as creator of the world. Material that was perfectly correct then may be so no longer. Finally, and perhaps most importantly, we never got to discussions on the third manuscript - what became "Book Two" in BoGJ - at all.
Sure, that section is as compatible as I can make it with both published and unpublished works that I had access to. Much of it was shaped by the discussions we had on the Loskalm sections of the original Heroes of Malkion manuscript, which ended up being subsumed into the later work, rather than simply repeated. So its as close to canon as it could have been, and very much influenced by others, not just something I made up on my own.
But that doesn't make it official canon, for all the reasons given above. It will almost certainly - heck, scratch the 'almost' - be contradicted by later official books. Obviously, my hope is that people won't be concerned by that, and this does seems to be the general attitude, at least among people that have written to me. There will, inevitably, be coverage of Loskalm in the Guide to Glorantha, when that eventually comes out, and that will be a different vision. Still, I imagine it's going to be a heck of a long time before another 170-page book comes out focussing on that particular kingdom.
Do with Loskalm as you will in the meantime.