Like their name implies, modular kits are modular and just like legos, you can build a lot of things with only a few different pieces. This makes the production much faster but there is a big drawback and that is that the things can get a repetitive look very quickly.
To avoid art fatigue, I often add a few unique pieces breaking the generic look and that is where problems can arise. Things that should fit no longer fit. In addition, you are at a point where you can not really get back to fix things - since it take a lot of time and could create problems elsewhere.
This is the moment when you have to do things differently - let's say by cheating a bit. If you can not fix something, then you can make it invisible, for example by hiding it. How?
You've got a little gap between 2 wall parts? Let's cover it with a pillar!
You've got two textures which won't connect properly? Let's place a rock on it!
May be you’ll find that is a lazy way to fix unexpected things, but it works, nobody will see it, it saves time and that is what counts. Something that has gone wrong, but can not be noticed as wrong simply does not exist as wrong.
Of course, there are different ways to solve a problem. You could un-build a part of the level and rebuild it with different parts to make things fit, but that's very slow and there is no guarantee that doing so won't break another part of the level. Creating an unique piece just to connect things properly is also another possible way, but I'm not fond of these solutions.
I like to keep my modular kits as simple as possible. What does it mean to have more pieces? Just a higher chance of making errors. Of course, If I want to make something architectural, that means modifying more pieces, but I believe that the most important thing is that if a modular kit is made, it should also be thought of for future potential users. A unique piece which was made to solve a certain situation in ones level used by another artist can become the source of a problem in this artists level.
In a team, you can always communicate with your colleagues to come to a name convention, an agreement for such pieces - but, for example, what about mod-enabled games? The external users know nothing of internal agreements on names for unique pieces and will find themselves with a broken kit to work, which gives them a to the highest unsatisfactory modding experience.
My recommendation on this topic is: if you are going to build a modular kit, you should make it simple and easy to use, not only for you, but for everyone else who will have to work with it.

