Does this happen on tiles in regular gameplay or only in simulacrum/MR test tiles? I use Phantasma constantly with several frames and have never seen this even with 3.4 punchthrough. My alt-fire projectiles always pop when they hit an object and the punchthrough works in the secondary explosion aoe. <my expecirience with punchtrhough on phantasma since it was released, but I've never used it in sim/mr test tiles.
Penetration through texture works on regular missions as well, not only in the "sim". Without МR, punching through textures still works with the "Seeking Fury" mod. I remove this mod and here is the result:
The "Seeking Fury" mod does not work correctly on Phantasma's Alt. fire and needs some work. This is definitely a bug.