I figured part of it out, the create_permission_url function from the Python Shopify API still only has the old admin url (shopname.myshopify.com) in it, so the permission url doesn’t work reliably for the new admin url (admin.shopify.com/store/shopname/).
I created the permission url myself without using the helper function and that worked. However, it turns out some shops are still on the old admin url, so now I’m at the client side Javascript part where I have to detect which shop url is being used and then generate the permission url client side. I’ll post an update here when I have that working.