I'm thinking, maybe not. They would have been produced in equal numbers in the first year (Hasbro confirmed that the two BBs, CJs and single BJ were to pad out the first year), but only the yellow one in the second year, would make it more common. Plus, BB was produced in the late 80s during the Chinese release of TFs, which we got in Australia in the early 90s.
So my thinking is, that even though the red one should be rarer, it would be in less demand to collectors, whom most would only want the yellow one. I actually acquired 2 red BBs before a yellow one, and before I eventually got a CJ. In todays TFs toyline, the red BB and yellow CJ would be given a prefix name (like Fireblast BB, or Flaming CJ) to differentiate their alternate colours, but back in the day with the new toyline, it wasn't considered necessary.
As such, they are only really considered worth getting to completist collectors. Anyone else who collects TFs, especially show-character collectors, wouldn't be interested in them, so the value *should* be less.
They make for good temporary substitutes (I had the red BB as CJ for quite a few years), but beyond that, I'm not sure if any non-completists have any interest in them.