I am modernizing the UI on every classic site I touch, but not groupifying them because of the complications you mentioned. Personally, I'm not a fan of private channels in Teams. The whole point of Teams was to move people AWAY from all these granular permissions we have in SharePoint. I have no idea how they're going to map permissions from a channel to all the tabs in that channel. Create separate groups? Individual named users with no groups. Are we going to get separate permissions on each OneNote section? Ick and double ick. If you need that level of granular permissions, maybe Teams isn't for you. Not every use case should be shoe-horned into Teams just because it's new and sparkly.
For us right now, Teams is for mostly small-ish group collaboration. If you need hundreds of people with complicated permission levels, use straight up SharePoint with traditional permission groups. If you're on traditional SharePoint and want to move to Teams, that's great, we'll set up a Teams site for you, migrate the content and delete the old site. But we aren't groupifying sites directly.