Whenever you go into a test flight like that you're going to have some level of risk and risk mitigation that go on. When I was working for engine OEMs we had FMEAs before first test flights. Not everything was working 100% perfect at first flight, and we did sometimes have realms we knew we needed to stay out of during flight. But you also can't move forward on a lot of the design of an engine/powerplant without actually flying the thing, and at some point you need to do that to make steps forward on the program. Each company/group draws the lines in different locations. Where they drew the line is not unlike what I've seen from other groups in the past and I can't necessarily disagree with their decisions for flight, especially for not knowing or being familiar with the details. This also isn't different from the decision matrix for other high-risk flights, such as ferry flights for a mechanically uncertain aircraft or first flight after maintenance.
In the NTSB report it said that they knew they hadn't identified Vmca for this aircraft, which I would expect to be very high given the small rudder and what seemed to be high thrust for the size/weight of the aircraft. I don't know what they were planning for approach speeds, but my guess is that they were using approach speeds that were more typical of the Quickie with the piston engine, rather than what you'd typically see on a twin. Approach speeds on a twin are much higher, largely to be well above Vmca and at/above Vyse. People who aren't familiar with twins often note how much faster we're going when flying in the 414 with me - I don't like being below 120 KIAS until landing assured and am usually 130-140 in the pattern (gear speed is 143, white arc tops at 147). The mitigation for the unknown Vmca was that if they lost an engine they'd pull both back to idle and land ahead. The only real thing that I see out of this from a decision perspective is that he deviated from the mitigation plan, and it seems to me was quite clearly below Vmc when he had the engine failure. Now whether the decision he made was better or not, who knows, but he walked away.
Design wise, from my turbine experience I do question the location of the engines relative to the forward/lower wing. I have no idea what sort of testing they did with respect to determining when the engine will stall, but manufacturers do wind tests to determine crosswind envelopes for turbine engines (specifically turbofan/turbojet). I would have wanted to see some wind tunnel tests to see at what AOA the engine would stall. Certainly it's possible that the crosswind gust combined with that wing design could've caused a flameout.
Personally I don't see any issues with their first flight decision and I think would've made the same choice. I would've wanted to look into that idle shutoff issue before the crosswind envelope flight that they were on, but might have decided to do other tests instead, focusing on higher speed items like climb/cruise performance. One thing I noted is the NTSB showed he had >1,600 hours of total time, but <50 hours in multi-engine aircraft. To me, that's an extra risk.
It's easy to second guess decisions when someone ends up in a crash, but nobody second guesses it if things go well. I don't see much point in Monday morning quarterbacking or questioning his decision to be a test pilot as a new dad (other than for him to question it, since that's a decision he needs to make). I certainly have tamed what I do to some degree post-kids, but I still do things like the ferry flight in the 414 after it'd been sitting for 6 years. But there were mitigations for all the risks associated with that, and (luckily) everything went right. I don't ride motorcycles as much, though.