Oz,
The primary reason to use our Stripe Commissions & Gateway plugin is so that your vendors can connect with Stripe and receive their commission to their Stripe account instantly at checkout. Admin then receives the remaining commission.
The WooCommerce Stripe will require that you pay your vendors their due commissions manually.
I looked over the Stripe Connect documentation and it does indicate that Apply Pay is now(recently!) available for Stripe Connect.
I’ll add this to the enhancement requests for our Stripe Commissions & Gateway Plugin.. but I cannot promise you the feature, nor a time frame. It would certainly be a nice option to have available.
Yes- leaving both Stripe payment gateways enabled will be confusing for customers. I’d recommend that you choose the more suitable one to use.