That has not once happened in 18+ years of existence of SH3 and/or using mods and/or applying any of my tools, S3F being the oldest (almost 9 years old).
Installing a game, playing it and modifying it does not require neither justify going down that road and all that hassle with a dual-boot.
That is makework unless there are other reasons such as running another operating system.
As Glenn always said: KISS - Keep It Simple Stupid. I appreciate that expression.
Maybe you are familiar with the American phrase "Sxxt Happens", I run several apps for another hobby that require Windows drivers, and if the drivers are not signed, they might get overwritten on a Windows update. That other hobby I put a lot of hours into, and if I am down for a couple of days, I could lose $$$ and the gigs associated with it that I have worked for 9 years to gain. I have always wanted to create a multi-boot setup; I have a wired network and NAS, but while Synology wants to claim it's simple to restore, the experience is stressful and not so easy. Forgive me if SH3 and running multiple instances are the catalyst I used to make the plunge lol, to learn something new, and will give me a new playground to experiment with other things and SH3. Something I didn't mention is that my current C: SSD is getting old, and this will allow me to upgrade from 500g to 1tb and use the old SSD for the playground setup.