There will definitely be deals where the standard agreements don't cover every term that is important to the parties involved. We have a few ways to address the kinds of nuances you're talking about.

The variables in the cover page are intended to handle the things that vary from deal to deal in most commercial software transactions. Those are basically the selectable boxes you referred to (or blanks to be filled in, etc).

For things not captured by those variables, there's a section on the bottom of the cover page called "Other changes to the standard terms." Users often choose an entry from the Language Library for that section, but they (or their attorneys) can write their own custom assignment language or whatever other specific term they need.

If there are a small number of edits in the "Other changes" section, it can be helpful to know that all of your agreements have their unusual elements in the same section. On the other hand, if a company or their attorney consistently needs to make a large number of edits in that section, it might be a sign that the standard contracts are not a fit for them.

When that does happen, we'd love to hear about it. That sort of thing is very helpful for us in thinking about what we can improve in future versions.