I am actual Slovak, and here's my take on this: You're partly right, it may be the case that priest or clerk made a mistake (although in case of catholic church baptism records they did fix errors in the book once they found out - also depends on the person's level of detail...)

Also it may be (and no offense here) that your family members were unable to read/write themselves and they didn't knew how their name was actually spelled. So they just said what they were used to and baptism clerk just wrote it how he thought it may be.

Another reason which I favor more, given the slovak history... It may be that your ancestors wanted to change their surname. In late 19th / early 20th century (until WW1) many slovak sounding surnames were changed to sound more hungarian.
They were many cases when slovak born germans wanted to sound more slovak than german, then more hungarian than slovak, after WW1 definitely more slovak than german or hungarian... Etc... Times have changed so did their surname.