I ran into this also, seems as if all we can do is make a choice from whatever TC offers us.

I did find we could do 'Multi-City' so I could then book a JFK-SFO-LAX-SFO-JFK and earn an extra 1000 EQMs but didnt find a way to request a higher fare so that as you want to, be able to Upgrade my tkt be it using Miles or on CO certain fares gives you FC then and there

1 better due to MC I wasable to take advantage of a Raffles Special if I wanted to, but didnt.So its not that bad .

Could be closer in to flight date and no ElCheapos left it will then offer the higher fares but then again maybe not