I personally went through the Stripe Atlas beta, no regrets. At the time the AWS credits saved me thousands of dollars. (On year 2 or 3 now, I don't recall)

In terms of what you're discussing though, I agree. Faced those same two issues.

What I did:

1. Keep utilizing my other stripe account(s). I have multiple web fronts, and each has it's own stripe account. No issue there, actually zero funds go through the Stripe Atlas account. All the accounts are merged through one login, which is easy enough to see.

2. Closed the SVB (Silicon Valley Bank) account month two of the company. Opened an account with Capital One Spark Business, no minimum fees and the customer service has been good. Moved all my stripe accounts to dump into that account.

Honestly, Stripe should really partner with a better bank.

All Stripe does is provide an easy way to setup the C-Corp and help with some information. You're still in charge of your business. I did enjoy the suggestions and reminders from Stripe Atlas regarding filings.