Update: It is working better now and they recently made many updates and improvements to the website functions and features.
Support said they're working on fixing the confusion with the recent login changes.
For anyone else having issues, these were the instructions (redacted):
"I've checked, and you have access to your websites with email1@gmail.com as the Agency owner. You’ve set up an agency named xyz with this temporary URL: xyz.app.lindo.agency.

To access the websites under that brand, you need to log in with email1@gmail.com at your agency: xyz.app.lindo.agency, not at app.lindo.ai.
I understand it might be confusing; we’re working on making it clearer."

I still get annoyed that there is a pop-up asking at least once per day if I'm satisfied with lindo.ai, so hopefully they'll remove that or limit it to a feedback box instead of a pop-up.