So one thing to understand about Stripe is that for every different domain, you will need to create a new Stripe account for it (within your main Stripe account). You can’t just hook your ONE API key set to many sites. Each of your domains need a separate Stripe entity. It is a little different than how you would handle this with PayPal.
Within your Stripe account, you can create new accounts (sub-accounts really) for each of your sites. Then those accounts will have a different set of API keys that can be used to connect to it. It will then create webhooks within those sub-accounts.
Is this something that may need to be sorted out for your setup (or you already have different sub-accounts that you are connecting to different sites)?