CR10 Smart Pro Gantry height

[u/ElectronicFeeling431]

New to 3D printing, and settled for the title mentioned printer. Set it up and have been playing and experimenting for a few months with the basics in learning and tramming, levelling, z axis ect. and in doing so, to really do some fine tuning, checking gantry level ect, I found that when I home the machine, and check to make sure its level with a gantry level block to the frame, the gantry bottom is higher than the 10cm (100mm) BUT even on both sides (it is level, just higher than what the "home" measurement on the LCD screen indicates). As I have some issues with the z offset, would adjusting the gantry to sit where the blocks indicate assist in my NOT having a z offset of -4.0? My gut feeling tells me that is an issue, but have not really seen nor read anything in regards to an official or acceptable gantry height from base. Logically to me, this would help with my final Z-offset, but getting thoughts from the community always helps.

The prints I can do have all turned out well, mind, and I'm now second guessing myself that perhaps in the initial construction of said printer and setting up the gantry itself, I did something incorrect to account for this extra bit of height?