Linux on external SSD?

So I have an AMD laptop and have Windows 10 installed.
The internal Samsung SSD has Windows 10 and my other internal HDD is for media files.

So if I where to install linux on my USB/External SSD, would my bootloader for Windows get screwed up?
Would i be able to change boot order and have Win 10 or Linux boot, depending on which SSD is chosen to boot from?

My question is basically will Windows bootloader remain unchanged after install.

Yes, unless specified otherwise the drive that you are installing to will have the boot loader installed there.

Say you install to the SAME HDD as your windows, yeah your MBR gets overwritten on THAT DRIVE and the new boot loader gets loaded on. But if you're installing to a separate drive, it wont conflict

You can install Linux on the SSD with a bootloader like GRUB that can boot the Windows installation from the other drive. Then just put the Linux SSD first in your BIOS boot order, if you mess up or unplug the drive you will automatically boot into Windows.

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Is the external drive USB3.0? Performance wise if you're just checking out Linux then 2.0 would be fine but if you're doing anything serious on it then I'd suggest you'd want USB 3.0 transfer rates...

When I am about to install, I get this:
"Warning: The partition is misaligned by 3072 bytes. This may result in very poor performance. Repartitioning is suggested."

Do I keep going? Don't know how to fix the partitions.