I ended up finding a fix so I could have 64K Allocation Unit with RedNAND and still have access on Windows.
After doing the RedNAND setup, I backed up 0x0 to 0x300 to file with HxD Hex Editor (via the physical disk option) then used EaseUS Partition Manager to format the larger FAT32 Partition (which is my data and not the RedNAND) as FAT32 64K Allocation Unit
Afterward, I used HxD Hex Editor to open the disk (Physical Disk Option) then I overwrote 0x0 to 0x300 with my backup from before the format. Afterward, I could read the SD Card again in Windows. ChkDsk gives the partition an ok and shows it as 64K so it is good to go now. the 3DS can read it fine also, A9LH still works and RedNAND works also. All my installed games still work also.