In the case of rule-based manufacturing, when 95% of the time you use a common rule to define drill depth or even tap depth based on the thread parameters, you can use a UDF to drive the feature based on the thread specification. This is true only for non-though holes of course. Two parameters that can be automated are thread depth (less common since it depends on the assembly interface) and the drill depth (point or shoulder) depending on the tap used and the clearance required. The relation can be written with the UDF into the feature's relation (rather than part relation). And at that point, yes, the relation will "freeze" the values to your company's "rule" if you will. The relation can always be removed or varied. Part of that relation can determine if it is a bottom tap or not using if IF statement. Be aware however, that changing values in a hole feature seems to rewrite the entire feature by replacing everything instead of changing everything. You can only tweak a few dimensions without this disassociation, but replacing the hole size will generate in essence a whole new hole.
Therefore, Tom's recommendations is a valid one in that making the hole a revolve, for instance, with a cosmetic thread, you have more control over the feature. You can do this with your intelligence built in using the UDF interface to interrogate the designer and then provide the solution.
The real advantage tot he true hole feature is the internal annotation structure. If the annotation note related to a hole feature is important to you, you will want to continue using this. Otherwise you will have to structure something similar on your own.
In general, this may be a lot of work that isn't worth it. I still have a notebook by my side that covers all my design rules. I would have likes a tap clearance value for non-through holes in the hole tables that would drive the initial depth of the hole in relation to the thread depth and maybe a switch for bottom tap or conventional.
