It depends on the gyms and their instructors. In my little town, aside from tae kwon do, there were only 2 real options for striking instruction: boxing and muay thai.
The boxing coach has training a few golden and silver glove winners and an Olympian. Plus, it was only $25 a month through the city's parks and rec department.
The muay thai coach was a certified instructor under a Lumpinee champ and was 47-0 in his fights in Thailand, plus had MMA experience.
The price was right for boxing, plus it was 3 hours a night, 5 nights a week, I could go whenever I wanted. But the boxing instructor told me I wouldn't spar for at least a year and he hated MMA/kickboxing/anything besides boxing. So I knew he'd never teach me boxing in an MMA context.
The muay thai instructor was more expensive and his classes were less frequent, but he was actively training fighters for MMA and allowed me to spar during my 3rd class.
If I wanted to train for boxing, the boxing gym would have been a great fit. But I was interested in MMA, so there was no question.