For what it is worth:
I got the same errors…I took a WIO-E5 mini and put it on a very simple custom board that was castellated and had a boot and reset switch…If I did as the wiki said under the End Node section:
That is hold reset, click connect then release reset I seen the same thing you are seeing!
I decided not to do that and just hit connect…When doing so I got the hex file to load fine without any warnings or errors…
Also found that If I compiled the code in STM32Cube IDE and loaded it that way download worked too.
I am finding however some code issue with the run sequencer as my console in the IDE keeps responding
Target is not responding, retrying...
after I hit run in the IDE