Would you be willing to consider capping the per-subscription cost? For instance, "0.5% of your subscription price, at most $x/month/subscription"? That would keep it reasonable for low-cost subscriptions, and have high-cost subscriptions pay more, but the cap would make it feel much more reasonable to use Stripe Billing even for very large subscription costs.

With a structure like that, I'd want to use Stripe Billing for every customer, rather than considering any kind of special arrangements for high-value customers.