From a security perspective, any elite status will do, so that's not an issue.

Neither carrier officially offers TATL upgrades for free, so don't expect much there. If you are flying from SFO to Texas you'll probably be on CO if you pick SkyTeam, so you should try for CO elite to get the upgrades there. That being said, the SFO-IAH route is pretty hard for upgrades, so don't expect them.

Lounge access for ST E+ is only valid for same-day international travel. That means you don't get access for your SFO-TX flights, though you would for your SFO-France flights.

I don't see any indication that DL/CO flights wouldn't earn EQMs on FlyingBlue, so I'm not sure where that came from.

You can earn CO EQMs on Alaska Air as well, so that may play into things depending on where else you fly out west.

Overall, I like CO, but the 40K miles for ST E+ is pretty nice, and the OpUp chances are better on the home carrier for the TATL runs. Combined with the fact that CO upgrades are pretty hard to come by on the west coast runs, FB sounds like the right choice.