Revocation of Global Entry privileges for Customs violation

As the Global Entry only pertains to Immigration and not Customs

I'm not sure where you get this impression from. It is a program run by U.S. Customs and Border Protection and as part of your privileges, you can complete your customs declaration on the kiosks and subject to less immigration and customs inspection.

one would expect the withdrawl of Global Entry to be because of an Immigration violation (e.g. misuse of Global Entry) rather than a Customs violation.

Customs violation can also be a misuse of Global Entry. Usually, one would have made a false customs declaration (in your cited case, the customs form asks if you are bringing any fruits to the U.S.).

The eligibility criteria also specifies you could be ineligible if you

Have been found in violation of any customs, immigration or agriculture regulations or laws in any country;

Actually I also believe that she was subjected to the requirement for increased TSA screening on future flights (even domestic).

I find this unlikely that she is flagged for additional screening (compared to most non-GE passengers) for simple customs violations, e.g. carrying an apple, that usually only carry civil penalties.

However, she would lose her TSA PreCheck privilege, which would have entitled her to less screening at TSA, that was linked to her GE membership.

She can still apply for TSA PreCheck offered separately from Global Entry, which to my knowledge does not bar people with civil customs violations. But if she has a criminal record like you said (but I find that unlikely), then she might have difficulties.

And on a related matter, now imagine that she subsequently tries to enter a foreign Country having acquired this Criminal Record:

Besides the fact that I doubt she has a criminal record from simply carrying an apple, assuming she does, then she would be ineligible for some visa-waiver programs, e.g. Canada.

Many countries ask about criminal record but also civil customs or immigration violations on visa application forms. Countries do care about customs violations (that's why many countries merged immigration and customs). She will have a more difficult time obtaining a visa; but it might not be too difficult if she can provide adequate explanation and show she has learnt from this.

We know very well that Immigration violations commited anywhere in the World will automatically show up on our passport record,

I don't find any basis for this assertion. There are data sharing agreements with immigration violations and sometimes also criminal records (e.g. US-Canada, or to an unkown extent, Five Eyes in general); but in general it is not true other countries have automatic access to backgrounds of foreign nationals.

But it is a bad idea to lie to visa or border officers since they can and do ask other countries for confirmation in case of doubt or in need of random controls. Lying (by ommission or even mistakenly) can cause you to be banned for a long time.