Brown has been urging the governing FIA to reconsider the rules that have allowed what he has called an A and B team collaboration.
Champions Red Bull won 21 of 22 races last season and closer cooperation with Visa Cash App RB, eighth in 2023 as AlphaTauri, could see the sister team become far more competitive.
Brown, in an FIA press conference at pre-season testing, said he did not know of any other sport that allowed co-ownership of two teams competing against each other.
Horner, who is fighting for his own future in the face of allegations from a female employee about his conduct which he denies, reminded reporters in the same conference that Red Bull also owned two football clubs in the Champions League.
Austria's RB Salzburg and Germany's RB Leipzig both reached the group stages of this year's elite European club competition with the latter in the last 16.
Horner recalled also how late Red Bull founder Dietrich Mateschitz saved Minardi from collapse in 2005, renaming it Toro Rosso, and how Red Bull stayed when manufacturers left and supported the sport through the COVID pandemic.
He said Red Bull should be applauded for that rather than "derided"'.
"The two teams are totally separate. One is based in Italy, one is based in the UK. The one that is based in Italy has a far larger turnover of staff that end up in Maranello than end up in Milton Keynes," he added, alluding to Ferrari and Red Bull.
Horner said the relationship between the Red Bull teams was "far less tight" than some others with their engine manufacturers.
"We expect them to be a competitor, not just of the rest of the field but of Red Bull Racing," he added.
"There are no pre-set rules, no agreements between the teams. I don't understand the noise that's being created about it... for me, it really is a non-issue."
Brown added in the same FIA press conference that, while Red Bull were 'playing by the rules', the sport was continuing to evolve with a budget cap in place and should aim for 10 independent teams.
"If the intent of the cap is to have an equal playing field... then the way the rules are currently written aren't the same for everyone," he said. "We now need to address it and the FIA needs to address it to the rules."
