I have 3/8" anchors and a piece of 3/8" threaded rod going down to the anchors. When not using my M4, the anchors are pretty unobtrusive or I can quickly unscrew the threaded rod and pop in a 3/8" hex bolt instead to keep the hole clean and then the only thing protruding up is the head of the hex bolt.
If needed later on, I can always get a bit of quick mix cement and fill the holes back in (drop in anchors and all) and it’ll be like nothing was ever there.
I wouldn’t worry about that offset for now. The difference the offset makes is likely pretty minimal and likely only an issue when making cuts closer to an anchor. Getting a frame set up and making cuts is much more important. You can always go back, make changes, and fine tune things later if you’d like.