Very few people use the hybrid mode, and some things may not work properly. One possible reason for this, is that apps may not be loaded in the correct order. Using the normal mode, extensions are loaded in a particular order. Also, if there are any bugs with hybrid mode, they are not normally found and fixed.
It depends how you remaster.
If you just add extensions to a cd, all should work properly.
If you do a genuine remaster, you may have some of the same issues with hybrid mode. Most extensions should work. I did a remaster with just a few extensions, some time ago, and it worked properly.
The only way to know for sure, is to experiment.
You may even be able to fix some things. See if you can come up with some way to get things to load in the correct order.
I experimented, some time ago, with combining a group of extensions into a large extension. Most worked. From memory, some didn't, I think because of things were not loaded in the correct order.