Yep, the book is clear that :25 supersedes :40 even if some don’t agree. I would still propose just going to :25 after all penalty administration with the option for :40 on B fouls when the game clock is starting on the ready inside of 2:00. We already have the option for the offended team to start the game clock on the snap inside of 2:00, so why would this be any different?
I agree that the rule states that :40 is the default, but is set to :25 under certain circumstances - ergo, :25 supersedes :40. However....
bama's scenario: A calls a timeout. After the time out, there's :25 seconds on the play clock. The ball is marked ready for play and the play clock starts running. If B jumps offsides prior to the snap, there is an officials time out under 3-5-7i due to a defensive player, which does not fall under the :25 superseding rule as per 3-6-1(a)-1(e) Exception 2 (man, that just rolls off the tongue...).
The timeout was over. The ball was marked ready for play. The play clock started running and needs reset ... 3-6-1(a)-1(d) no longer applies, because it was just stopped due to the foul, not the timeout.
That being said, I'd support the rule to be changed to reflect what you're saying (or what steely dan was saying, if the game clock is on the ready or not) but I disagree that it is what the rule currently says.
The situation where the rule is really dumb is: game clock running, snap is imminent, B jumps into the neutral zone. Now A gets a new :40 with a running game clock and can potentially eat 1:20 in total dead ball time unless you apply 3-4-6 and hold the GC until the snap.
Maybe the defense shouldn't have jumped into the neutral zone. That's on them. There's lots of dumb rules, but they are the rules.