I do this via registry keys.
Although you have to use the target of the .lnk file and not the lnk file itself.
Find the target of your shortcut, I'll use "C:Windowsnotepad.exe" for this example.
If you want to apply to all users on the computer, use the registry key:
HKLMSOFTWAREMicrosoftWindows NTCurrentVersionAppCompatFlagsLayers
If you want to apply only to your user account, use the registry key:
HKCUSOFTWAREMicrosoftWindows NTCurrentVersionAppCompatFlagsLayers
The name of the value will be the target, so in this case "C:Windowsnotepad.exe" (without the quotes).
The value type is a REG_SZ.
The data is a space-delimited collection of the following flags: (without the quotes)
"DISABLETHEMES","640X480","HIGHDPIAWARE","256COLOR","DISABLEDWM","RUNASADMIN"
And one of the following: (you can't use 2 of these together)
"WIN98","WIN4SP5","WIN2000","WINXPSP2","WINXPSP3","WINSRV03SP1","WINSRV08SP1","VISTARTM","VISTASP1","VISTASP2","WIN7RTM"