When I asked the very nice people manning the Select Executive help desk, I was kindly informed that the coupon was actually good for the "base rail fare" of any given ticket whatever that may be - i.e., biz class on the Acela is perfectly fine, and you would only pay the flat upgrade cost to go to First Class with the companion ticket.

That having been said, I've never actually tried to cash in those coupons so your experience msy very.