Would it be possible to use Stripe Atlas to create the LLC, bank account etc and use Stripe normally for handling the payments side for the subscriptions.
However, if a marketplace came with the application. To use a 3rd party for all that comes with it. IOW, not wanting to use Stripe Connect for various reasons that make sense to the business.
You're welcome to have your company do business with anyone you wish it to do business with. We do not obligate you to use any Stripe product; we feel like we should always have to earn your business.
(We in fact go further than that; Atlas actively goes out of our way to help our companies take payments outside of Stripe, for example getting paperwork together to e.g. publish apps on the App Store.)
However, if a marketplace came with the application. To use a 3rd party for all that comes with it. IOW, not wanting to use Stripe Connect for various reasons that make sense to the business.