The machine is MSI Titan GT80 SLI UEFI laptop.

I multiboot Win one, Windows two (clone of one) and now Ubuntu. During the install I removed the primary Win SSD and Ubuntu modified the EFI partition of the clone Windows 10. This is bizarre, since I explicitly directed the install to go to SSD #3 and assumed the install would not touch either #1 or #2. Yet it did.

I had to run diskpart, assign a drive letter to EFI part and then remove all the ubuntu stuff from there. I think that's a flaw in the install process. Why would it modify disks that are clearly not a part of its install process?

Probably because the firmware determined which EFI partition it will reference. Bad assumption on your part I would suggest.
I've never seen the sense in having more than one on a machine.

That seems to be the default, at least with the Ubuntu Grub2 on an EFI install meaning it installs Grub files to the EFI partition on the drive it sees as sda. See post 5 at the link below. As far as I know, nothing has changed since then.

https://ubuntuforums.org/showthread.php?t=2344948

The site below discusses this 'bug' in detail with numerous users having the same problem. Posts 19-23 by the same person who posted at Ubuntu Forums gives some details on his attempts and seems to have a possible solution given in post 23? In post 19, he mentions doing an install EFI with Fedora to sdb which apparently succeeded so it might just be Ubuntu? Good luck.

https://bugs.launchpad.net/ubuntu/+s...y/+bug/1396379

I create a snapshot of Windows on a monthly basis so that if I get a virus or MS releases some broken update (like 1809) that wipes out drivers, I can always instantly get back in the game by booting off the clone drive. It's near instant and there is no recovery or trying to fix it. It's not cheap as I have a SSD that's on standby and only used for the purpose of snapshots as often or as rarely as needed.
Over the years I found out it's the best compromise. Data is expensive and so is days of downtime.

Now I added Linux to this equation but it's there is no snapshot. I might back up critical data.

My UEFI machine will not let me add any Linux drive to its BCD configuration, MS locked it up. So during the boot cycle I have to hit F11, get the list of bootable devices and select Ubuntu. It's either that or I can go into BIOS, make the Ubuntu drive the Boot choice #1 and then configure Grub to chain the other Windows disks.

My point is, any distro should not access a drive other than where it has been told to install explicitly and put Ubuntu in another drive's EFI partition. It only did it to the clone disk since I had the foresight to remove the primary Windows 10, otherwise I would have ended up performing this procedure there as well:

https://linuxbsdos.com/2015/09/05/ho...in-windows-10/

run diskpart select Windows disk, select the EFI part and then manually delete the Ubuntu directory that should not be there.
Really not a big deal but took me a while to find it. If both disks EFI partitions are affected, the machine won't boot anymore until I remove one of them.
Took me a while to diagnose this.