Hi there.I also hesitated at this point since I m used to mods containing data, docs and pick from mods folders.
BUT.. Just put the main patch 4 folder in sh5 mods folder.
If you look at the filestructure you can see also that mods are modded. Can check this by looking at real nav in patch 4 folder , realnav in mainmods folder ( the one you downloaded and probably stored somewhere) and compare with the realnav you get as a result in the main sh5 folder.
The exepatcher u just get a new snapshot ( with the changed file sim.somwthing I think)don t bother that u get the patcherprogram again. As far as I know it just replaces itself but that doesnt matter since its a standalone program same version.
Ofc there are other mods updated too, I didn t check them all
You can do that if you like but not neccesary