Why would he have issues landing with work permit?
I overall have no opinion on this 'nikkah by phone' issue, except to note that it's not going to have any legal force anyway. If it works for them religiously/culturally, by all means. They could get pretend-married by exchange of pipe cleaners for all I care, mind, so perhaps my view on religious stuff doesn't much matter.
As for whether IRCC will find this weird or think nikkah essential - as long as they have other relationship proof and are living together when applying are the main things, mind. (Side note: I'm not sure if it's worth telling IRCC about the 'online nikkah' - no legal significance anyway, and not relying on full religious/traditional).
That said: as I mentioned before, it may be best to have 2-3 months living together to apply. Since he will have work permit, no major rush, and that gives time to document life together and paperwork etc.