Reordering or dropping transactions is a non-issue. All you need to covertly implement Asicboost is dropping 2 random tx on the left side of the tree, and 2 on the right side (out of ~2000!) That's enough combinations to find enough partial merkle collisions. So at worst these 4 dropped collisions will be included in the next block because the next miner, even if he also implements Asicboost, will statistically almost certainly drop 4 different collisions.
And it's not true that a "significant" number of blocks are empty. Only ~2% of them are.
Furthermore the reason some blocks are empty is not due to Asicboost. It's because after a new block is found, there is a small delay until a miner can assemble the new set of txs, and during this period of time the hardware has to mine on something (empty block).
Above all, it would be in an Asicboost miner's interest to include as many tx as possible in order to gain a ~10% increase in revenues from tx fees!
So, no, I disagree that Asicboost is a "problem". It's not. It looks like Gregory Maxwell either misunderstands/misanalyzed the "risks" or is simply dramatizing the situation for his own personal (political) reasons which would be part of his plan (Blockstream's plan?) to attack and discredit large-scale miners in the overall debate of Segwit vs. Bitcoin Unlimited.
Asicboost could hypothetically become a problem only if (a) mining profit margins became very thin caused for example by a multi years period of BTC losing value or remaining flat, (b) if somehow the 3 Asicboost patents (Bitmain's, KnC's, Hanke's) were never licensed to anyone else, (c) if the patents owners actually did evil things by abusing their patent rights, and (d) while all this chaos is happening everyone else sits on their hands instead of ignoring the patent and adding the optimization to their ASICs for the benefit of Bitcoin's health or survival if it came to that...
It's very unlikely that (a) (b) (c) (d) all occur at the same time.