You certainly can't count on it. Sometimes some airlines (I don't know if JAL is one of them) may offer upgrades for money at the gate, but they may try to simply lower the business class fares last-minute to attract last-minute business class fliers and fill the cabin up that way. And even if they offer upgrades for money at the gate, they could be more expensive than a booking cheap connecting cross-Pacific flight in business with cash on another airline. (The fewer business class seats are left, perhaps the more they'll charge for them? Perhaps some airlines might even do it via a bidding system?) And/or they may have their own system of upgrading their own frequent fliers which fills up the business cabin (again, I don't know the specifics for JAL).
Are you aware that if you want to pay enough miles you can get any business seat on the plane with enough miles (several times more than "saver" redemptions), but only on flights flown by the airlines whose miles you're using? For example, you can't do with Avios for AA flights, you can only do with AA miles on AA flights (there it's called "AAnytime" redemptions). This is not possible with Avios on Tokyo to Vancouver, because the airlines that use Avios as their own "miles" currency (BA, IB, etc) are all based in Europe, and thus don't operate flights between Asia and North America. (In any case, I'm not sure whether BA/IB/etc have such "last minute" awards with Avios on their own metal, like AA and UA and DL do, or not.) .
I don't know if any airline that flies Tokyo to Vancouver that you can transfer MR or UR to (such as Air Canada) offers that or not. But like I said you'd need to use the same number miles as several "saver" business class awards to get one of the "anytime" business class awards.
It's hard to "count on" upgrades no matter how you're upgrading. If you absolutely "need" a particular kind of seat, you have to find a way to get it outright (with miles or cash) at booking time if you want to be "certain" of it. Upgrades are always qualified by "if available".