In my experience most projects that need to worry about things like this are too big for a high level of consistency to work. Either that, or the design is sacrificed to make the code easier. Whenever a designer looks at a page they say "left a bit, down a bit" until they're happy with it, regardless of consistency.

So, yeah, use rems or ems if it makes your life easier. Use a CSS preprocessor with lots of helpful variable names and functions. And just don't worry about it.