Same behavior here.
Everything works just fine. I have 3 different Win10 PCs and I can program my MRKWAN1300 boards using the usb or serial1 interface normally. Using the Arduino IDE software OR Atom OR VSCode. Everything works just fine.
I use the same WIN10 PCs to deal with Arduino UNOs, and have no issues also.
One weird thing I see on the picture attached on the first message is that you have MANY COM ports at the same time (COM4, COM5, COM6 and COM7). In my system I can only have one at a time. When running normally I have a "Arduino MKRWAN1300" and when I switch to the bootloader (double click the reset button) I have a "Arduino MKRWAN1300 bootloader", but never both at the same time.