It looks like Notepad++ now (as of 7.6.3) supports the portable apps plugin structure in the way we hoped (inside the portable folder structure).
What's weird is it starts, after updating through the PA launcher from 7.59 to 7.6.3, by acting like none of the plugins are there and presents the new Plugin Admin interface. Once I use that to install plugins, and restart the app, the Plugin Admin disappears from the Plugins menu and all of my recent opened docs, both the history on the menu bar and the opened files, are lost/closed.
Any thoughts? For now I think I'm sticking with 7.5.9 as the trust factor is not yet strong for the 7.6.x series.
I highly suggest manually adding plugins to the correct location. To my knowledge, the plugin manager has never properly worked portably. Just because it happens to be included doesn't mean it works.
Sometimes, the impossible can become possible, if you're awesome!