Matt & Michelle
While I have dreams of one day being an AMEL expert, I have spent many years certifying engine installations (JD, CAT, Volvo and Yanmar) in heavy equipment. To get a definitive answer to your question, you really must ask Amel/Yanmar. When Amel contracted with Yanmar to use their engine (or Volvo for that matter) the Amel engineers had to submit an installation design based upon Yanmar's Installation Requirements Document (I believe it is at Revision 17.2.A). Yanmar does a pre-installation review of the data submitted and provides a go/no-go decision. The first Yanmar engine can then be shipped to Amel for test fit/install. Amel then installs the engine, and Yanmar engineers show up and run a gazillion tests across typically 5-7 days (cooling, fuel flow, vibration, exhaust pressure diff, blah blah blah). If the tests pass, Yanmar gives an Authorization to Supply, ships Amel engines, and stands behind their 2000Hr/2Yr warranty. The point is to ensure the engineering design is maintained and will perform as expected.
The orientation of the exhaust elbow will be in that cert document. As will be the fuel line lengths, fuel pump model/placement, electrical harness length, key switch location, vibration model/mount, overflow size/location/height, exhaust hose size and length, intake size and length, etc/etc/etc/etc. All the sexy data is in that document....even the mass-spring spectrum graph....sweet!
Does it matter? The Japanese engine manufacturers DO NOT do random decision making. The part is the way it is installed for a very specific reason in THIS INSTALLATION. You have one data point that shows that it has not mattered based on how that boat has been operated. Maybe there are risk mitigations that are overly conservative. Maybe they just have not hit yet. The only way you will truly know is to ask Amel or your local Yanmar rep to look at the cert document. Another option is to reach out to the Yanmar America Certification group in Adairsville Georgia. They are good guys and may be willing to give you guidance or a definitive answer.
Talia - SM#208