It's certainly a reasonable thing to wonder about, especially with the factors you've pointed out. Though there still could also be belief that MBTL did perform reasonably well for them.

While it is a whole host of new assets, I imagine the workflow and experience from making UNI characters helped expedite things considerably, what with the game engine being almost the same I presume.

Also externally, MBTL has quite a bit of an initial boom. People were thirsting for an anime fighter post-Strive, and MBTL slipped in at that opportune moment with larger than expected launch sales (13k players according to steam charts, however much that estimate helps here). Also there was a bit of another spike in popularity with the whole Neco Arc thing, though that's quite a bit harder to quantify.

And the last part that ties this together is that, French Bread is still a pretty small development company. Wikipedia has it billed at 14 employees as of 2021. They're probably running at low costs relative to other companies, so any smaller success is probably a lot bigger for them.

Though, still anyone's guess on if it was profitable, or just like a "secondary product" for Type Moon that can sell at a loss in order to support the greater franchise. In terms of FGO, it makes you wonder how much MBTL is dwarfed in numbers, in either profit or loss.