A couple of physics issues are in play here. Backwash has been mentioned.
There is also a low pressure zone that forms at the intake, causing stress on the little rubber impellers. depending on hull, high pressure can form at the exhaust through hull.
Water beats air every time.
Newer diesel engines have the monitoring systems almost on peer with diesels. All my pressures and temps are on a common data bus to my chart plotters.
In short, if they say don't use a generator underway, don't.
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