I wouldn't say it's outright "wrong" .. but then.. I hesitate to even attempt such a placement of my branding on a client's web site. If the goal is to promote your web building business above everything else... then it's actually "right" in that respect - even if it is ugly.
If the client(s) is/are aware of the placement and have no arguments regarding it, then I guess the boss is right.
- Aesthetically, it is confusing to readers. How do they know which logo represents the company/parent company/subsidiary/etc. Just brand confusion for the clients and visitors. But again, if the client(s) fool heartedly agreed to this.. that's their branding nightmare, not your employers.
- Liability - any claims regarding issues or problems resulting from use or content on the site may just find their way to your employer first and foremost. It's tradition that any branding in the upper left corner is the company responsible for the web site... so If I get cheated or lied to, that's the company I'm going to contact, complain to the Better Business Bureau about, etc.
Other than these, there's just a whole litany of design issues which aren't traditionally anything one can foist upon someone that doesn't understand design. Things like branding conflicts where colors are just not harmonious or style dichotomies... None of which could feasibly be argued without seeing actual imagery. The sad truth is, if 'the boss' just doesn't "get it" you may be stuck with that horrible positioning.
Kind of reminds me of the old phone book trick... name your company "AAA Design" so you appear first in the listings. It will work... but it's "ugly sales" which is a real thing.