The tool uses ADB to do the job, too, the same commands you could enter yourself, so it does the same things, see TapDebloater/src/main/java/org/lorenzoantonelli/tapdebloater/core/AdbUtils.java at master · Lorenzoantonelli/TapDebloater · GitHub.
But it’s a technicality, I think. In the end the Apps getting treated this way are effectively gone (for the user).