Hi. I just got back from a trip almost a month ago with the same camera and noticed the same thing. Fortunately for later adopters Sony figured this out and has an option to turn off this "what you see is what you get" in the EVF for the A65 and A77 (menu option to turn off VF predictive lighting). But those of us with the A55 are still dealing with it, if shooting with other than Ikelite strobes connected to the housing. (I have z240's.) On the other hand, the a55 is limited to a 1/160th sync speed, so you can only get 'so' dark of backgrounds regardless...if we had the 1/250th of the A65 and A77 without the VF fix, we'd be even worse off.
By the way, I have z240's and was firing with one synced (cabled), but firing in manual mode, and the other optically slaved. I can confirm that even though the strobe is electrically connected on manual mode the A55 still doesn't "know" it's there. I suspect any i-TTL-connected strobe (or even a TTL-connected strobe but with the housing set to "manual" firing mode) will still cause the EVF darkness problem.
At least the AF points still work although we can't see through the EVF because it's turned down. So for non-macro type stuff (larger subjects) sometimes I could just point and watch whether or not the AF center point locked. Never entirely sure what it was locking on though (e.g. eel nose vs. eyes).
1) I didn't try popping the flash inside the housing. I did try it on land before the trip and confirmed that it didn't pop up enough to trigger...which means the little contact sensor that says "it's up" isn't engaged. So I'm not sure this would help.
2) Sony's advice to 'frame in A mode then switch to M for the shot' is of course completely useless outside of a macro/tripod type environment. Fish move. 
Really the only things I found that would work were to use a good focus light and/or turn on the aiming lights on the strobes so you can illuminate the subject a bit. You'll still struggle to see in the dark VF, but at least that gives SOME hope of finding the subject. The aiming lights on the z240's and my focus light all do detect flash and turn off so as not to influence the final shot. But I am starting to seriously consider picking up a small DS-51 and using it as the 'triggered' strobe but have both z240's optically slaved. That would get back TTL ability and hopefully let the EVF be brighter knowing a strobe is indeed connected. At about $300 for a used DS51, it's a lot cheaper 'fix' than upgrading to the A65 and getting the new housing...
Other things I tried that didn't really help: boost the ISO so for the same exposure time (1/160th) the VF is brighter, and turn down strobes. Helps for short distance shots, but means that you can't get dark blue backgrounds. Use the rear screen instead of the EVF - both do the same autogaining, and being somewhat farsided too trying to near-focus on the rear screen vs. looking thru the 'distant focus' EVF tunnel just added more problems. And last...shoot a lot of wide angle / hyperfocal (Sigma 8-16mm) and plan on cropping to finalize the framing, since after all we do have plenty of megapixels. I know, not very satisfying...