Problem is that SDCard Reader are not normal USB devices, but windows look at it as whole device and canćt just eject SDcard from device without removing whole device.

I use Internal SDcard Readers and also have USB Sticks that are Card readers, they all get warnings that device is in use. Therefor I replaced it with app called Zentimo https://zentimo.com/ previously I used Safely Remove Device https://safelyremove.com from same company and never looked back. It will show you if MM access device and why.

Note that I am not paid or any affiliate with them just simple user of their app that can't imagine how to work without it.

After finishing a resync, I try to eject the device (SD card reader) but it claims to be "in use". This happens whether I try to eject via MM or Windows. If I close MM, I can eject normally through Windows.

MM 4.1.29.1910
Windows 10