I know I can enter horizontal and vertical scales as percentages, but the baseline can only be entered by points. Is there any way to go around this with a percentage value?
Probably not. Baseline shift works in your current unit of measurement, points, millimeters, etc. It does that because the Baseline grid itself is defined in 'pt' or 'mm', and not in percentages. However, you can do the math with a calculator and find out what percentage you need, also, if you type in '1 pt' in the box, then go back and type in 400%, see what happens. This may or may not be helpful as the purpose is not very clear.