If you want to install an aftermarket mainboard in your Ender 6, you will most likely lose easy access to the SD card slot. This mount allows you to use an inexpensive SD extension cable, and mount it back in the factory location. From the outside, you can't tell the difference, and you can flash firmware without turning over your printer. Should work with the stock screen or the TH3D LCD conversion kit. Been using this on my Ender 6 for almost a year, paired with a BTT SKR E3 Turbo, and the TH3D LCD kit. Never had an issue.
The SD extension I used is linked below. You will need to pop off the housing to expose the small PCB. Then place the PCB between the top and bottom mount plates, and screw it in place using the factory screws.
https://www.amazon.com/gp/product/B01D9JIUU0/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&psc=1