This was your choice to make, and you made it.

It seems to me, as a DM, if you want to account for companion upgrades you can:

1) Elect the SWUs and use them for that purpose.
2) Gift GM to your spouse and improve your position for u/gs
3) Take the 25k extra SMs and use those for mileage u/gs

Thus Delta provides options for those who want to upgrade companions outside the standard upgrade process. It's just a matter of whether someone values those options over others.