Interesting angle that I hadn't considered.
That said, I don't think it's the same. Vehicles and fighters are classified in various ways (power/weight, but also experience, e.g. pro and amateur classes) because otherwise the competition becomes 'who has the best engineering team' and not 'who drives best'; or 'who has most fighting skills' and not 'who can overpower his opponent through sheer force/mass'. It's purely to keep it interesting and/or exciting.
In this case, I interpreted the argument made in the OP as 'it only becomes an achievement when the computer constrains itself to the boundaries the human has by its nature'. I don't see the point of that. An F1 car is unarguably faster than 50cc kart. If we talk about 'who can drive the fastest', it doesn't make sense to say 'it's not a 'fair' comparison'. It is, and the F1 car is faster, period.
The nature of the past match was 'who is the best Go player, no holds barred'. Call it the UFC 1 of Go. Back in 1994 in UFC 1 there were no weight classes, no restrictions on techniques - the question was 'who is the best fighter'. It's not like after that event the sumo guy said 'yeah well I can't move as fast because I'm 200kg, so we'll only know who is the best fighter after a jiu jitsu guy fights me but doesn't move faster than I do'.
I guess there is more nuance to the debate than I originally thought. I still think it doesn't make sense to impose artificial limits. We might have tournaments for humans and tournaments for machines in the future, just like we have nascar and F1. But there is no mistake who is the best player.