It doesn't immediately look like an App store version referencing issue, because the form you are using:

tell application "OmniFocus"

Should work with both.

I personally tend to use:

tell application id "OFOC"

which also works with both. (Note that it is case-sensitive).

I don't have an App Store copy, so I can't directly test whether:

tell application id "com.OmniFocus.MacAppStore"

is case-sensitive.

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