I'm having a similar problem, having recently moved to a dual monitor setup wit ha WIndows laptop. The laptop screen is a 3000x2000 13" screen, so very high DPI, and the monitor is a larger but only a 1920x0180 screen. I can adjust the zoom in RStudio for either monitor, but I'm not sure if there's some sort of adaptive solution I'm missing.
(Windows 10 Pro 1803)
EDIT: ref. also this thread and this comment. I can see this has been issue for a while and that you're well aware of it 
I'm finding that the ideal zoom for RStudio in my setup matches that for Windows: 100% for both RStudio and Windows on my external monitor, and 175% for both RStudio and WIndows on my laptop display. Perhaps a future version of RStudio could have an option to read the current display's zoom setting on boot and on changing displays? (I don't have much Windows dev experience; I shouldn't presume 
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