Hi Michael,
The fact that discounts currently apply to customers rather than
subscriptions is a known issue that will absolutely be addressed as
part of multiple subscriptions.
We may or may not continue to support discounts being applied to
customers.  We will certainly need to support that for backwards
compatibility, and I suspect that some merchants may find
customer-based discounts to continue to be idiomatic, even in the face
of multiple subscriptions (eg, "Foo has a 10% off for life discount,
regardless of what subscription(s) he is on").
But, we know that we need coupons/discounts to be able to be applied
to particular subscriptions, as part of a feature-complete multiple
subscriptions offering.
Regarding your second point about shared customers and subscriptions,
I'm not aware of better examples that we have to share at the present.
 However, if you're having any issues with your implementation, we'd
be happy to chat with you about it and possibly look at code snippets.
 If the public forum isn't the best place for that, feel free to reach
out to 
sup...@stripe.com.
Cheers,
Jim