I feel like CPanel is still better even with the higher fees
Can't say you're wrong. Especially for people with little experience in hosting, it's easier, which is also the main reason why cPanel has higher fees.
Look at it this way. The more you want in and from a car, the more you will have to pay. Same for a control panel.
As for a clear documentation on how to install a letsencrypt certificate... -> You didn't look well in the documentation it's quite easy. But things have to work first. Seems some services were not even working in your case after an hour. That's an odd thing, because I presume you don't have a system that's so very slow. Normally after half an hour things should be working. So it's a pity you ran into that issue.
As for managing multiple domains on 1 account, that's very easy it's even the basics of DA, just add the domains in the domain manager, you can have 10 (or 20 with the plus). I don't understand your problem with that, I presume it's only with the importing from CP.
Migrating mail only can be done with imapsync. However I don't see any CP doc about that so quickly either.
Anyway, maybe you will be back later on some time. DA isn't that bad. But can take some work in some cases, which is also why it's cheaper.