InDesign does line spacing based on point size and leading. The default is em + 20%.
If you have your ascenders and descenders crossing over, they are probably just too darn long, and you need to rescale the font or redefine the em size.
An "average font" has a cap height of about 0.7 em and x-height of about 0.5 em, with ascender of maybe 0.75 em and descender of maybe 0.25 em. The 20% extra added by InDesign is then all white space.
So if you deviate from the typical by more than 20%, well, yes, you'll get clashes. Either expect users to change the leading in serious publishing apps, or make the font smaller on the body.