Use the same save file for different copies of a Switch game

Yes you can. You will need both Switches.

From the Nintendo Help pages:

On the source console:

1. From the HOME Menu, select "System Settings" > "Users" > "Transfer Your User and Save Data."
2. Select "Next," and then "Next" again, then select "Source Console" to indicate that the content will be transferred from this console.
3. Select "Continue," and then finish the following preparations on the target console.

On the target console:

4. From the HOME Menu, select "System Settings" > "Users" > "Transfer Your User and Save Data."
5. Select "Next," then "Next" again, then select "Target Console" to indicate that the content will be transferred to this console.
6. Select "Sign in" and choose to sign in using your Nintendo Account e-mail address or sign-in ID.
7. Enter either the e-mail address or sign-in ID associated with your Nintendo Account, and the password, then select "Sign in" > "Next."

On the source console:

8. Wait for the target console to be found, and then select "Transfer."
9. The transfer process will begin, wait for this process to complete.
10. Once complete, select "End" to complete the process.
    • If no users are left on the console after the transfer is complete, a placeholder user account will be created.

They also include a helpful video on how to do this:

As for if you can play different saves on different copies of the game, yes you can.

Since the cartridges don't change version like in the N64 days, you have 2 choices. Starting at 1.0 on a wifi disabled switch with the physical game; or playing on the latest version on digital/wifi enabled switch.

The only way to play 1.1 (or any version between 1.0 and latest) would be to

1. Emulate it
2. By some kind of sorcery flash your own cartridge with a 1.1 rom.

Both options seem like pretty hard to do as of now. So I would say you will have to give up. The records that are recorded in the 1.1 version are now pretty much untouchable and skips/glitches that were available only in the 1.1 version are now unusable.