Al least this should be possible from within Linux.
So start Linux, from where you start dosbox or wine for your patch.
Than boot into AROS with kexec-loader:

http://www.solemnwarning.net/kexec-loader/

If this is not working you might somehow load grub2 without going throug bios reset with:

https://github.com/error10/kexec-reboot

More info:

https://wiki.ubuntu.com/RapidReboot

I assume that rebooting after running your command will reset the clock multiplier, making that option for booting AROS nonviable. As AROS's kernel complies with the multiboot spec (IIRC), the problem becomes more generic: find a way to boot a multiboot kernel from your environment. Or find a way to launch GRUB(2) from there without rebooting.

I have a dedicated AROS box and Im really happy with it, but Ive recently set up another AROS system for a different purpose.
Now it does the job nicely, but I have a nice ultra small form factor system Id prefer to use.
The problem however is this small system is a bit older, and as such only "officially" supports pentium4's and the 1st few core2 cpus. To circumvent this I have an unofficial bios+software solution. This lets me run any 65nm cpu, my choice being a 3.06ghz c2d e7600.

Big upgrade from a 1.86ghz c2d e6300, but the problem is the software side of this upgrade bath is a Win32 command line tool.

As such, my question is:

Is it possible to invoke a command line tool via a very minimal Win32 layer running (hxrt or similar) on a stripped down dos, and then have that dos start the aros boot process? The idea ultimately being of course to start AROS at 3.06ghz (without the software the cpu is stuck at a 6x multiplier).