If you are generating Gcode yourself, by hand, that is awesome. I know a lot of experienced, long career people that have never used anything but automatic generation via a CAM package. You will learn a lot about how things work this way. (I use a cheat sheet at this point. I have been spoiled by competent CAM tools)
Before setting ANY of the machine variables (GRBL or Gcode standard ones), write down the original values so you can reset them. The FAQ explicitly states that G54-G59 are intercepted by CM, as the machine settings may be used by CM-- or Carbide Create-- itself. (https://docs.carbide3d.com/software-faq/list-of-supported-gcodes/) If you use another sender, they will be available to you, but restore them to the original values before going back to any C3D software. GRBL does not recognize G52. Again, it does recognize G54-G59, but, I can not emphasize enough, record the existing values before changing them and restore them before using any of the C3D software. (your mileage may vary. I have not had any problems doing this, but make no guarantee)
Some of the limitations are due to CM using particular features for its own purpose. Others are due to stuffing a modern control scheme into what is essentially a pre-1980 technology processor (the Atmel based Arduino hardware) limiting the feature set for GRBL.
For direct control of the machine, another sender can be used, but you will need to deal with tool length probing yourself (it has been discussed previously on this forum), and may want to set travel limits (default is off for soft limits, or at least was when I got my machine).
Most CAM chains don’t have any issue with the unimplemented/blocked features. They generate Gcode using what is available, trading more work up front (location calculation and so on) and longer gcode files for multiple coordinate systems and canned cycles.
You really can use any serial-capable sender. I have used PuTTY for manual control, and even used it as a file sender for a few things (my wasteboard surfacing job, for example).