Can anyone else experienced with Wrye Bash make a statement too? I think I don`t fully understand what this kind of merging actually does and what the consequences and maybe downsides are.
When WB merges a mod, it copies most of the content from that mod into the Bashed Patch. I write "most of", because WB is smart and only copies the parts of a mod that is not overridden by a later-loading mod. There are a number of advantages to this. One is that you have less active mods, but the most important one is that WB is able to combine parts of different mods into one record.
E.g. ModA changes the damage of a sword while ModB changes its textures. Normally, due to the rule of one, only the latest-loading mod that changes one record (the weapon) wins, so the damage change of ModA is lost due to ModB loading later. But when the Bashed Patch merges those mods, it is able to take the damage from ModA and the texture from ModB and merge both into the weapon's record in the Bashed Patch.
Note that WB can only merge mods that add no new content, but only changes content from its master (like ModA and ModB above do). WB can also import from a mod instead of fully merging it. Importing is more or less the same, except that only certain aspects of a mod (like textures) are imported into the Bashed Patch, instead of merging the whole mod.
There aren't many downsides, though one is that other mods can check for whether a certain mod is active in order to establish compatibility, and if this mod is merged and deactivated, the check will fail. Another is that bsa files are only loaded if there is an active esp whose name matches the start of the bsa's name. If the esp is deactivated, the bsa is no longer loaded - but this can easily be fixed by renaming the bsa to match another active esp.
What about the load order? If they can get merged into the Bashed Patch it must be irrelevant where these merged ESPs come in the load order, as they are at the end after merging.
Load order is important. If two mods both change the same stats of a record, the last-loading will win, and in this case, be merged into the bashed patch.
What if I often make changes to these ESPs? That means I need to rebuild the Bashed Patch every time I make change to a merged ESP, right?
Generally, yes.