it is strongly discouraged to do touch and goes in any retractable gear aircraft
Why? I regularly do T&Gs to stay proficient in various landing techniques and I always fly a retractable (172RG).
Yes, you need to reconfigure the a/c pretty presto, but isn't that what training is all about ? Proficiency?
PS: if you are referring only to Bonanzas and Barons then there may be a valid reason (though I can't think of one) - I have no experience in either.