Seems like you need this board then, i.e. board = node32s.But it doesn’t change the problem you’re having.
Could you follow this advice and comment out that statement in your esp32_out.ld file?
Also it seems to me that this board does have a normal 40MHz crystal (according to this and this p. 30, which means that your initial modification should be removed. You can remove the whole sdkconfig.h file, it will get re-generated.