This is the biggest issue for me as well, but I've mostly learnt to live with it by not scaling the HiDPI display in sway. What I do instead is scale the XWayland applications when possible.

For me the only XWayland apps that I want to use on the HiDPI display are Chromium and VSCode and both of them have options for scaling (e.g.: "--force-device-scale-factor=2" for Chromium; "window.zoomLevel" for VSCode).