Yeah, that is unfortunate that it’s not directly possible with the new system.
However, I’ve just done some testing, and it looks to me like there is a workaround that could be scripted and included in the V3D exporter.
If you take your shape-keyed object and split each shape key to its own object, (duplicate the object for each shape key, set that key to 1.0 and the rest to 0, then delete all the keys, deleting the key set to 1.0 last), you can then apply the modifier, then join your objects as shape keys, and re-apply any animations that you had.
This method doesn’t leave the modifier intact like the “bake modifiers” option in the V3D exporter currently does, but I’m not sure how you guys are doing that or whether the same approach could be applied here with my method described above?