That's an entirely reasonable change. Of course, it does make inter-team logistics potentially more difficult, but I'd recommend that if you're using a non-red/non-SB50 connection for main power, that you build and carry an adapter to the quasi-standard red SB50 connection.
There are also clones of the SB connector available from other vendors (like the
AMP Power Series from TE connectivity). It might be nice for FIRST to permit those as well—consider asking on the Q&A. (If FIRST doesn't grant permission, the brand markings on the connectors will make clear who the manufacturer is, for inspection purposes.)
The Anderson SB Smart, SBS, SBE, SBO and SBX connectors may remain illegal, even if only 2 poles are installed. The Q&A should clarify this for greater certainty.
Also, as a public service announcement, note that the SB connectors (and AMP clones) are keyed: the traditional red ones won't work with anything except red and black (universal)
Edit: and apparently pink also.