Hole depth vs. screw length won't help. You need screw engagement vs depth, and then you need to know if the engagement is sufficient for the application and if that engagement removes the lead-in chamfers on both the fastener and the hole.
It also might be difficult if the mating isn't between the threaded hole and the fastener. If the mate and alignment is with the mating part that is being retained then this task will become very difficult.
At best one could generate a report of all mating conditions and then look at all the features to see when one is to a threaded hole and the other to a threaded screw. Then, supposing that the screw actually has a thread feature, one could track those. I don't recall ever adding that feature to screws; instead it was typical to use a parameter for the user to select the correct screw part number.
If the screws aren't mated with the threaded holes then one might need to do a search of all geometrically aligned hole/fastener pairs, then check for axial overlap (how one determines the actual threaded part limit on the screw will be tough - some screws have two cylinders, as in socket head screws and not all screws are fully threaded, so it might require creating that tabulation relative to the underside of the screw head.
If you want this to happen, I expect it to be a significant software development effort.
What I have done is to group each item with the retaining hardware so that each installed item can be individually verified for appropriate selection, correct engagement, matching thread, and quantity, including any washers.
Most users tend to assemble all the major parts and then follow that with all the fasteners into one giant indecipherable mess. This jumbled system has lead to multiple fasteners being placed into the same hole - a pattern fails on a piece part and gets redefined, then the screws that follow that pattern collapse into the original hole, so a user notices the assembly has a bunch of empty holes and patterns the fasteners again, or simply assembles far more screws one at a time.
