Ok, I figured it out by myself. For anyone curious, yes it's possible to just use Bashed Patch from Wrye Bash in these cases. But you have to add the Bash Tag {{BASH:Invent}} to the applicable mods. Then, they will show up in the 'Import Inventory' step when building/rebuilding the Bashed Patch, which in the end will contain correctly the merged NPC inventory. For example, both the mods 'Morrowind Imports' and 'Bal Ruhn SE' changes the inventory of the same seller NPC in Windhelm. In order for both of them changes to take effect, they must be included in the Bashed Patch as described. (But note that it's not a *plugin* merge between them, just their *inventories* merge, therefore their esp's still need to be 'ticked on' so the game can load the mods fully.)