Design flaw in Esoteric DV-60?

That sucks. I gather that you keep it plugged in b/c it has a standby function and loses its sonic mojo if running from a cold start. (I had that issue with a Lamm Ref line stage- you were supposed to leave the power supply powered up but lightening strikes always made me nervous, and i pulled power during strong electrical storms or if I was going to be away). It took quite a while for it to come back 'on song.' I don't know and didn't research what the PS Audio products purport to do, or whether they claim to offer any protection.
Here I have a whole house surge, and run a large 10kVA isolation transformer that also has surge protection to the panel feeding the dedicated lines for the system. My assumption is that with a powerful enough strike, all bets are off. Surge protection can only do so much. You should add Jea48 to your list of electrical gurus. Hope you get it sorted without pain. 

I have the Eaton on the main panel it was around $100 plus the electrician’s time to install it which wasn’t much, because he was doing a whole lot of other work here. For the main system, everything runs from dedicated lines fed by a Controlled Power Iso transformer which has its own large surge protection board. In both cases, there are pilot lights that indicate when the surge protection should be replaced. (MOVs become ineffective). I don’t have any point of use surge protection on the main system components, but have them on virtually every appliance and on my second system. (My Quad 57s stay plugged in and ’on’ all the time, and for those, I use a ZeroSurge from Frenchtown, NJ, a company that I believe holds some patents that it licenses to others for this type of surge protection).
I still think if you get a really close strike you are toast, but the surges and spikes should probably be within the range of protection of most of these devices. I think the cheapy power strips with surge protection-- which don’t tell you anything about the state of the MOVs-- are about worthless. And, I don’t know what the point of use type do to the sound. It doesn’t matter as much on my second system, since it is a vintage, bandwidth limited system anyway, but I was always reluctant to stick point of use surge protectors on the main system. I have a few sitting around, from Furman, to old Richard Gray stuff that was used in a big projection system many years ago (along with his 240 volt step down) and never used them for the main hi-fi. I know @Eric Squires is a big fan of the Furmans.
Agree re your decision not to invest more in yet another repair without getting to the bottom of this.
I gather none of your other components have been affected, only the Esoteric?

One thought if neither PS nor Esoteric have a solution is to ask whether a beefy external power supply can be substituted. i know this is done with computers and other gear that uses wall warts- but perhaps the board in question involves more than simply supplying DC power. I don’t know if the schematic for your unit is available on line (they company may not like it being posted if it isn’t) -- however, if it is available on the Net you might get some thoughts here on whether such a mod is possible. (Or consult with somebody near you that has good electronics chops).
Another is to see if Esoteric would be willing to extend you some sort of accommodation to buy a new or refurbished unit of another model with a more substantial power supply, given the travails you have been through.