Well, I have a moment and will give you my opinion on this and we will see if there are opposing views that follow.
At first glace you look at what you are proposing and would say "it does not matter, both reference ground so whats the difference".
But there is more to it than that in my opinion and it is also stated in the NEC as such. (I know you are in Canada and probably have the same opinion that I hear on these ships all the time which is "We don't follow the NEC") (But just like I tell these guys
"They make these rules for a reason").
The NEC states that the grounded current carrying conductor shall be bonded to earth via Grounded Electrode Conductor at your first source of disconnect.
(Which basically means, for you building service you install the correct size ground rods and correct size wire to connect the ground rods to the neutral and bond this at the main disconnect of your building)
This is the only place the utility service neutral should be grounded to earth.
Its been a long time since I have been proficient finding my way around a code book but I would say without hesitation "NO do not bond these neutrals together".
If you want to read more on your own, google Artical 250 of the NEC and make your own assessments. (But be warned, if you are not use to reading this sort of thing make sure you have a bottle of aspirin handy and try not to pull out to much of your hair while trying to understand what it actually says)
Off topic but interesting none the less: (and I would love to hear feadback of others on #1)
1) you said "of course" when speaking of grounding the secondary side of your control transformer.....well, that is a topic that bounces around out here like a ping pong ball. Not everyone on these ships grounds the secondary side of control transformers. Some do, but other will leave it floating and use 2 pole devices to break both legs.......and others will leave it floating and only use 1 pole devices still
(That last group is scary and concern me very much but they live among us. How fun is it when you turn off a breaker to change a solinoid coil while standing in salt water only to find the panel was built by the last group I speak of and you find out the hard way that one leg still has power. I have been there and those are the days you wish you could have a beer onboard)
2) Back in the good old days, the NEC did have an exception that you could bond the metal case of you residential stove and clothes dryer to the neutral of a 3 wire cable and not have to run a separate ground wire. I don't believe that exception exist any longer as most municipality's require the use of 4 wire outlets for these appliances now. (will have to look one day and see if the exception is still in there.)
Anyway good luck with your endevors and we will see what others have to say on the subject.
Cheers,
BCS