From what I've heard, it wouldn't make it totally incomprehensible somewhere else. The foundation is the same, if that makes sense. Some people may, however, look at you oddly or laugh at how you say something.
I learned Peruvian and Ecuadorian Spanish for the first 2.5 years, with a little exposure to accents from Spain, and then thought the teacher who took over had odd slang, since he spoke Mexican Spanish. The next teacher I had sounded like she only knew Spanish from textbooks, so it was rather weird-sounding as well.
In college I took classes where I got to hear Spanish from Argentina and Spain. So I tend to get odd looks regardless, since I can't remember where I picked up a certain word, but usually if there's any confusion on meaning, a native speaker can explain how *they* would say it, and then we're good.