Some users have already encountered this problem as well:
If a PMI is selected in a 3D-PDF, it doesn't highlight the linked feature (surface) per default. Apparently, you need to set 3 settings, this is universal across the latest releases and different platforms:

https://community.adobe.com/t5/acrobat-discussions/pmi-linked-faces-in-3d-pdf-do-not-highlight/m-p/12734910
https://acrobat.uservoice.com/forums/926812-acrobat-reader-for-windows-and-mac/suggestions/45017893-bug-pmi-cross-highlighting-not-working-for-3d-pd

While two of them aren't critical, the deactivation of the protected mode of the Adobe Reader is not an acceptable solution if you run these PDFs in a commercial environment.
Are there any other solutions? Any ideas how to solve this?

Since I see 3D PDFs as the future standard medium for 3D info exchange, I hope there will be a better solution. Unfortunately, on the community board there are no real proposals.