I don't think this is the case.
I re-molded a VERY old JM Custom to do exactly what the OP is talking about long ago. You can see the difference in the geometry. If I put the 9c in the new JM, it will allow for holstering with the safety off, and it doesn't stop the safety from being deactivated while in the holster. Keep in mind the 9c isn't wearing a light, and so doesn't have positive retention, but I don't see how the geometry would change.
I inquired about this when ordering my latest M&P JM Custom Light Bearing holster. This was part of the response:
" the full guard will not reliably lock the safety into place, and for that gun I would suggest you not trap the safety on. If you choose the w/ safety version, it will be covered on the body side. Yes it will work just fine with a non safety version. We have an enigma compatible option in the drop down menus. Thanks"
I'm not sure why they don't recommend it, because I really like the holster I re-molded. That being said, JM Custom probably knows what they're doing better than I do, so you'd probably want to ask there.
NOTE: I have noticed that, when allowing my modified holster to self-activate the safety, if I depress the trigger just slightly to impersonate a foreign object (finger/clothes/etc.), the safety will not fully mechanically engage if the trigger is not fully forward.
UNLOAD your gun thee times, and then play with this to see what I mean. If the t
rigger starts moving before the safety
FULLY engages, the gun will
still fire because the safety isn't allowed to mechanically engage. I like the safety being turned on and locked, but I don't think it's likely to prevent a discharge if one forgets to manually engage the safety and a foreign object gets the trigger moving before the safety is fully engaged, which seems quite likely to me in this scenario.
I hope that made sense.
The gun with the smooth slide cover plate is a 9mm 2.0 compact, and the textured plate is on an original m&p9c. I plan on adding a safety to the 2.0, so I bought a holster accordingly (JM Custom IWB 3 Light Bearing for TLR-8AG).
Top picture is old re-molded holster and bottom is new factory JM configuration. In the side-by-side, the unmodified factory holster is on the 2.0 compact with the smooth slide plate. Sorry for the funny orientation of pictures.
The safety is in the on position in the top picture and in the off position on the bottom picture.