you could but its most often the "folder" that's listed as a conflict and not the specific "file" so the warnings are often precautionary in nature and not saying the same files are always replaced although that sometimes happens.
lets say the conflict warning is about the objects folder and you open the objects folder in both mods and compare them but don't see the same "files" within it being used, well then there is no conflict its just a common "folder" that's being changed.
with something like that you can create your own merged mod by copying the mods on top of each other to combine the files since nothing is actually replacing the other mods files. this is how you go about creating your own custom mega mod.
now if you find that two mods do in fact change the same "file" then you have to make a decision on how to proceed, you can pick one mods version and do without the other or you can "merge" the two mods together by adding the changes made to that file by one of the mods and add those changes to the other mods file so it contains the changes of both mods together in that one file. in order to do this you need to know exactly what those changes do so you can judge if the merged file still has the desired affects that both mods were trying to achieve.
understanding exactly what the changes do also is a great help if there is a true conflict where you must decide which change to keep if you have to give up the changes that one mod makes in order for the rest of the mod changes you want to work.
when things are greyed out it just means you must install some other mod first before a greyed out mod is no longer greyed out and its safe to uninstall it.
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