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This is normal and nothing to be worried about.

The PHP File Change Scanner does not scan all file on your site but only those matching the extensions to be scanned in its configuration.

Previous versions of Admin Tools did not include the .phtml extension. This was added in 5.4.0. Therefore the old scans of your site did not record the locations, sizes, modification date and signatures of the files with a .phtml extension.

The new scan, taken with 5.4.0 does see them. Since they did not appear in any old scan Admin Tools labels them as "new". This is the expected and correct behavior.

That said, you should really not be using the .phtml extension. This is a leftover from PHP 3.x. That's not a typo. I am really talking about PHP 3 from nearly 20 years ago, not PHP 5.3 from nearly a decade ago. The .phtml extension was deprecated in PHP 4 and there's a good chance hosts will stop parsing files with these extensions as PHP in a short while, if they haven't stopped already (some hosts have, indeed, stopped treating .phtml as PHP executable files).