I set up my dowel system right from the get go as I figured to go CNC and gain the production advantages, dowel assembly was a must. And you can't beat dowel assembly for speed in my opinion. I do add an assembly screw between the dowels on a stretchers just in case of glue failure on a two dowel joint, but other than that all dowel only in the joints.
I think dropout is on the right track and you should start with the drill block and make sure it is alligned to the spindle correctly. There is an offset that the cnc uses to tell it where the router head is in reference to the drill block. If the refference is off in any of the four directions you will get a missalignment. and you could have two missalignments that add up to a perfect allignment.
The way that I set mine was to make a 1/4" x 1/4" x on a panel and then make a hole with a 1/8" bit right in the center of the x. make sure that you place the 1/8" bit in the drill block in the same location where you will place your 8mm bit for dowels. The small hole in the 1/4" x 1/4" cross makes it easy to see where and by how much to adjust. Keep tweaking the offsets till the block alligns with the spindle. Then run the pattern 5-10 times on different spots on the table to determine accuracy on repeatability.
Once this is working well you can go to the boring machine and start checking it. I have had machines that were not perfectly parallel to the table all along the bore path and while this did not affect the flush front to back it would through the flush side to side off some.
I started with a maggi 21 spindle, then an accusytems H23 and was able to get acceptable results with both but not perfect every time. The overlay doors and hinges and slides of the euro construction system was always enough to make everything look perfect after doors and drawers were on.