It CAN happen that you'll get lumps and bumps and little puckers - usually when that happens to me I assume it means I didn't have things properly flattened out when I basted.
You don't need to do SITD with FMQ at all - it's optional, especially if you've basted thoroughly. I skip it if I'm doing an all-over FMQ pattern. I really only use the two together if I'm trying to accent some of the piecing lines, or if my FMQ is done like a medallion in the middle of an open block, then I'll SITD around things like that. Normally my FMQ stitches won't cross or touch my SITD stitches, except in small spots, to move from space to space.