By all indications, R is a First/BusinessFirst fare. The mileage earning on this fare really has nothing to do with what type of fare it is, Revenue management sets the fares, rules and inventory availability, and the OnePass department decides, somewhat independently I assume, how many bonus miles / EQPs each specific fare class will earn.

These R fares are replacing what used to be the cheapest of the Z fares, which were usually for the seasonal (summer/Xmas) BF fare sales.
For example, as part of the DL fare match, CO is offering a $998 (+tax) r/t fare on EWR-LGW starting 11/15:
RL5S3E, 50 day advance purchase, $400 change fee, Sat. night stay requirement

The next cheapest fare is also R:
RLR50APE, $2326 r/t, with 50 day a/p, $300 change fee and 7 day stay requirement.

Then come the Z fares:
ZR30AP3E, $3065, 30 day a/p, refundable/changeable, 7 day min stay
ZR14PE, $3330, 14 day a/p, $200 change fee, no min stay

Then come the D and J fares (though FWIW, the D fare is rather restricted on this route...).

And note, I haven't seen any R fares on domestic routes, only BF routes, but that doesn't mean there aren't or won't be.

Why R could be automatic upgrade to BF
 

CO has said a few times in the past that they have a "problem" with passengers booking full Y seats on transoceanic flights and cancelling at the last minute.

I've even been known to do this waiting for a waitlisted upgrade to BF to clear.

But if R becomes the international equivalent of the "AU" bucket for elites, a person could book full Y, automatically get upgraded into BusinessFirst (in J), and free up the revenue to sell in coach ...as long as there's space available in BF. Because most J transoceanic travel is business travelers who are typically there because their arrangement with their company guarantees that travel be confirmed in J, they'll continue to buy J tickets. Your flyers flying on their own dime will probably continue to buy discounted tickets (or discounted tickets + mileage + fee) and the smaller population of high-fare paying Y Elites being able to automatically get moved up.

I know if I bought a full Y and was automatically upgraded, I'd be good to go on that flight. If I bought a full Y today and waited around for the upgrade game, there's a 50/50 shot that I'd fly that route. And if someone else bought Y, it could still be sold since their "iffy" reservation is held in J where flights are sold for a premium anyway.

Why else introduce a subclass in BusinessFirst with less mileage earnings?

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.