Honestly, and with all due respect, I'm not sure I understand any of your post. CO already has sub-classes of coach with different EQM earnings, so they're just extending that concept to the front of the plane. It makes perfect sense that they don't want to give you extra miles for purchasing such a deeply discounted BusinessFirst ticket.

CO has never said anything about offering free upgrades on Y fares on BF routes, and I'm sure it'll be a cold day you-know-where before they do that. And you should be aware that in many, if not most, cases, these new R fares are significantly less than Y fares (the EWR-LGW Y fare is over $3K, compared to $1K for the cheapest R fare). The R fares are very restricted, and the Y fares are completely flexible. Very different target markets.