A few key points with Emirates upgrades:
Fare type matters a lot.
Flex (or Flex Plus) fares generally require fewer Skywards miles to upgrade and are more upgrade eligible. Saver fares can be restricted or require more miles. So yes, booking Economy Flex instead of the cheapest economy can absolutely change upgrade cost and availability.
You need Emirates Skywards miles to upgrade.
Amex MR (Canada) does transfer to Emirates Skywards, but you’ll need to confirm the transfer ratio for your specific card. It’s often 1:1, but double check in your Amex portal before assuming.
If it is 1:1, your 91,000 Amex points could potentially cover a one way upgrade from Economy Flex (since you mentioned 91k miles required in that case).
“Last minute email” upgrade offers
Those cash upgrade offers closer to departure are capacity controlled and unpredictable. Sometimes they’re great deals, sometimes not. Fare type can still impact eligibility, but the pricing is usually dynamic.
A380 matters
On the A380, Business is a very solid experience. Direct aisle access, onboard bar, lie flat seat. For someone with leg issues, that makes a huge difference on a 13+ hour flight.
Realistic strategy:
Book Economy Flex if the mileage upgrade requirement is 91k and confirmed as available.
Immediately transfer Amex to Emirates and request the upgrade if “upgrade with miles” space is showing.
If upgrade space isn’t confirmable now, you can waitlist and monitor closely.
If you can only swing it one way, I’d personally upgrade the outbound so he arrives rested.
No magic hack here, but using Amex → Emirates and booking the correct fare bucket is probably your cleanest path.
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