Yeah I'm pretty sure the things you've describe is why people are upset. GMK does have a lot of problems (The pretty bad trays, spacebar warp, inconsistent texturing and rarely keys being sorted wrong ) but this is a vendor/designer issue (there might be instances where the colours can't be put on to keycaps but I think that's up to a designer to know if the colours are achievable), as the designer or vendor who started the group buy has to approve the colours before the set ships out (That's why GMK Dracula took so long I believe). There was also some drama recently about GMK Moomin and Red Dragon (made by the same designer who has had a history of mismatched colour sets I believe) where some of the colours were completely wrong as well.
The only guaranteed way to get a set perfectly matched is if the set is only using stock GMK Colours, but if you like a design make sure you go and see if a designer or vendor has a good track record of well matched sets, as you will probably be in good hands.