Pavel,

Until all miners update (firmware or hardware), the change encourages
large difference in mining efficiency. And IMO it gives another
advantage to large mining operations in general.

Certainly, there would have to be changes for stratum, pool software, etc. But the monetary incentives align to all the changes needed. 

Remember, overt ASICBoost can get something like a 12.5% efficiency boost from toggling a single bit in the version (equivalent to 2 colliding work items), 18.5% from 2 bits (equivalent to 4 colliding work items), 23.4% from 4 bits (see https://arxiv.org/ftp/arxiv/papers/1604/1604.00575.pdf). In lieu of an explicit allowance of overt ASICBoost, the monetary incentives lead to odd BIP9 signaling, especially if 4 or more proposals signal at once. There really isn't a practical way to block overt ASICBoost without forcing the version bits to be some value.

In other words, the question isn't about allowing/disallowing ASICBoost at this point. The question is whether we want ASICBoost open or hidden.
 
You make a strong assumption that the new optimization is not
compatible with overt ASICBoost. If it is compatible, ASICBoost
doesn't help you with "defending against" the new optimization at all.
And it can be the case that the new optimization is based on ASICBoost
so you can make the situation "worse" by allowing it.

This would only be the case if overt ASICBoost were not possible at all. It is currently possible to use overt ASICBoost, so optimizations based on overt ASICBoost would also be possible unless something were done to actively block it.

> Certainly, if only one company made use of the extra nonce space, they would have an advantage.

Can you explain why the reality should be significantly different? In
sufficiently near future.

Market incentives, I would imagine. How quickly that would be is not something I'm qualified to answer.
 
We don't have to deal with any such theoretical situation now. You
proposal goes in opposite direction, by adding support for patented
algorithm. I don't know myself what the possible legal implications
are (maybe only for a subset of miners) so I consider it as an
unnecessary risk. At least before some conclusive legal analysis says
differently.

I'm not adding support as much as explicitly allowing what's implicitly allowed. Whatever risks you imagine for this proposal exist on the network currently, with unmodified BIP-141 and with modified BIP-141. The difference in adding the modification is that overt ASICBoost is explicitly allowed in the modified BIP-141 as to not hide it.

Jimmy