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This is an interesting case of spelling and pronunciation reflecting two different senses of the word's origin.   The mpt doesn't really belong there; the word comes simply from control.  

But control has changed its meaning over the years.   It comes from contra + rotulus.   The rotulus was a scroll, and contra-rotulus referred to an early form of double-entry bookkeeping.   Balancing one scroll of numbers against another.  

In European languages, controlling still means checking, auditing, proofreading.     In English it has come to mean dominating or taking charge.

In companies or governments that have a Comptroller, the job retains the old European sense of auditing, not the modern English sense of taking charge.   So the spelling of the job changed at some point, with a false back-formed etymology from French compt as in compute, which became count in English.

The comptroller's job is related to computing or counting rather than dominating, so his title took on a spelling related to counting or computing.

Thus you can pronounce it either way, but you're favoring one sense of the word by your choice.