I use alignment holes in my projects for tiling - I just completed a 6' (72") growth ruler on my 4' (48") CNC. I tiled it at 40" and did a 4" overlap (so it went up to 44"). Within the project I carved 1/4" holes in waste space of the project all the way down into the spoilboard at Y=0, Y=4", Y=40" and Y=44". Tile 1 included all these holes.
Then for tile 2, I moved the project down and anchored it using 1/4" metal dowels (which went through the project into the spoilboard) at what was 40" and 44" (which is now 0" and 4" for tile 2).
I moved my CNC to the appropriate X and Y=0 and confirmed that my 1/4" end mill fit into the first hole. Loosely clamped it. Then moved Y=4" on the CNC and confirmed the 1/4" end mill fits in the hole - using two holes validates both X and Y. Depending on your project you can do multiple sets of holes to confirm alignment.
You can see videos that describe this process here:https://www.youtube.com/watch?v=7ugAiQuJ-zo&t=191s