I have the same problem. I use 2 monitors plugged into my retina mac (running win10 via bootcamp). The retina display is set to 150%, the other 2 monitors to 100%. WinSCP never leaves one of my external monitors, but is reflecting the 150% scaling.
It has unfortunately made the app unusable for me, and I'm downgrading to the prior version now.
Need some way to toggle whether I want the scaling to apply in winscp or not, if the dynamic scaling is difficult to support. A major regression in the ux for users in this situation. I imagine this problem will become more prevalent over time as 4k monitors start seeing more widespread use.
As a workaround, set your default Windows scaling to 100% and override it for the retina display to 150%. Not the other way around.