Looks like the animations should not be imported on models with $staticprop, but should be imported on other models to get the correct rotations. I was able to fix this on my side, but it would be probably better to have an option to import only non-$staticprop animations in BST. In any case, thanks for helping.

That seems to be the case actually. Checked a couple of models and the ones with $staticprop were correctly rotated.

I checked that all of the meshes I have there are imported with animations. The issue is not the fact that the models are rotated in Z since that can be easily corrected, but that seemingly some models are rotated and some are not. This makes it impossible for my .vmf importer to import all prop rotations correctly.

On some imported models the Z rotation is wrong, compared to models loaded into Half-Life Model Viewer as .mdl and exported as .obj and imported into Blender with settings -Y Forward, Z Up. Decompiled .qc models were imported with the following settings: https://imgur.com/9VaNtI8

Here's a screenshot about the issue: https://imgur.com/d0W6eDa

Blue models are imported with Blender Source Tools, and grey models are .obj imports. On most models, the imported rotation is correct (e.g. CSGO models "models/props_vehicles/van.mdl", "models/props/de_inferno/bench_wood_new.mdl"). However, in some rare cases the Z rotation is incorrect (e.g. "models/props/de_mirage/bomb_site_tarp.mdl").

The same issue is in both BST 3.0.3 and latest unreleased BST 3.1.0. The models are decompiled with latest Crowbar before importing. The issue doesn't seem to be in Crowbar, since recompiling the decompiled .qc models doesn't affect the rotation on the problematic models.