Hello 66locort,
This all depends on the application. If its a rolled on system, then no, it will not hide the flaws but rather accent them or make them stand out like a sore thumb.
Depending on how flawed the floor is, it may need to be patched or even self leveled with cement. depending on its potetial use, we would use urethane fortified cement in floors where there would be heavy traffic, heat and water. Or we would use an acrylic modified if you where looking for a stained or polished look.
Maybe a poured self leveling epoxy or troweled epoxy system would work better in your case. Difficult to determine with out pics and reference on the flaws.
You definately have options but they aren't cheap. Imagine having your floor on the wall and rolling on a couple coats of paint. It'll look like a disaster. But hey, alot of guys on here and throughout the country do exactly that and are content. Question is, what is your expectation and how much are you willing to spend to reach it?