there are a few stupid rules they are told to enforce - but keeper shorts being black or your team colour isn't even a rule, nor are they told to enforce it.
i was at the zone leagues meeting when russel henry from NF put the keepers gear to rest - at the meeting it was decided that keepers could wear any shirts, shorts & socks they wanted as long as the shirt and socks didn't clash with their own team, the oppositions team, the oppositions gk or the refs. his words were "if a keeper wants to wear something ridiculous like fluro green shirt, fluro green shorts & fluro green socks, he can if he wants. why he would want to, i don't know, but that's ok". a few weeks/months later he sent out an email saying that they had re-decided that keepers now had to wear team socks, so couldn't wear whatever socks they wanted. the shorts were never brought up again.
in football, teams are allowed to wear clashing shorts. see the a-league - brisbane don't even have an alternate coloured pair of shorts because they don't need to change regardless of what shorts the opposition wear. both teams, both gks, and all refs could wear black shorts and it would be fine. this is why the fifa-regulated rule doesn't really make sense about under-shorts skins/compression gear needing to be the same colour as the shorts, seeing as though it doesn't matter what colours shorts teams wear.
the ref you guys had sounds a little loco. if he cuts a half short without reason, do you cut his match payments? does he understand that in first grade the whole stoppage time thing actually exists?