It's been a while but as I recall those are separate lists.
A "merge patch file" makes your game more unstable? Are you sure you don't mean a "merged plugin file" which is combining mods to reduce the plugin count? That can well result is a more unstable game if the wrong mods are merged.
A "merge patch" resolves record level conflicts and I have never heard of it making the game unstable. Without one, only the last mod to touch on the same record will get used, ignoring all other mods. With it, only the individual record conflict has a single "winner" and not the entire mod. Please see the 'Third Rule: The Rule of One' and 'Merge Patch File' sections of the wiki "FNV General Mod Use Advice" article. When in doubt, create a "Merge Patch" file for your overall "load order" anyway. If you add, remove, or change the sequence of plugins in your "load order", don't forget to rebuild the "merge patch" file again.
Post in the "Technical Support" sub-forum if you are still having problems with a "merge patch" file. If you really are having stability problems we want to hear the details.