Because you have an 8GB flash drive, I'd recommend setting up a persistant live session, meaning when you boot your computer via USB you'll get an Ubuntu session that will retain your files and preferences (background image, theme, etc.). I've tried installing Ubuntu to a pendrive several times and it would normally crash beyond repair when running updates, yet running updates within a persistant live session seems to work well. On your Ubuntu box you should be able to access the
Startup Disk Creator which will allow you to use an Ubuntu disc image and make your pendrive boot it. Ubuntu alone will take up less than a gig, you may want to grab the DVD edition which is 1.5 GB (includes GIMP so it's worth it), and you'll still have plenty of space for more software and files.
As for boot loaders, your pendrive will only boot Ubuntu, so not really an issue. Your non-Apple computers have a BIOS, where you have to make sure it's possible to boot from USB (Pentium 4's are a hit or miss, anything newer should be able to boot from USB). There are instructions here for booting Ubuntu via USB on a Mac. You may want to use UnetBootin on your Mac to make your pendrive bootable with Ubuntu.
If what you are looking for is like a portable virtual machine (which I doubt, because you said you want to modify files on your computer with USB running on a pendrive), it would be much more complicated for it to be OS-agnostic. Maybe using Qemu, but even then, you'd have to have it set up real well with emulators on the pen drive to be able to run a virtual machine on multiple computers/operating systems containing all the software to do that right on your pendrive.