My machine has hard limits, and when it homes it goes to the hard limit first, then moves the specified distance to the soft limit (35mm on the X). When I first got the machine I put a corner piece that runs along the edge of the soft limit and attached it so that I always know where my 0,0 is and can align pieces against it.
I havent had any issue in creating parts that fit flushly with others Ive cut on my CNC machine, and can easily queue up another to be cut without worry. I just shove the piece into the corner, then cut. On a number of those I do have to manually input the offset of the cut from 0,0 to get the cut where I want it to be, but I know that it can always hit it reliably.
Numeric positioning also helps me a lot when making sure I make the most of my materials. As different materials have different kerfs, I know what the minimum distance I can place and object away from another and still achieve a clean edge while maximizing the material usage. It may sound trivial, but there have definitely been times where an extra half a milllimeter has been the difference between being able to make the part now vs having to order another piece of material and waiting for it to arrive.