UGH! I understand you fully
MMV! Handshake issues are no fun!
It seems a very common problem for many users since it's one of the major issues between HDMI components for whatever technical reason. I'm experiencing it too between my current Oppo BDP-93 and Denon AVR-3808, but it's only related to bitstream audio in my case, not video. The audiosignal has a delay of about 1-2 seconds before it "locks" in the receiver, and thus intros of soundtracks are missing. No biggie, but still irritating. I recently connected dual HDMI cables from the Oppo and it aids the problem somewhat - one HDMI fed to my TV (sends video only) and another fed to the receiver (sends audio but also video).
Same as you I am curious aswell about the AVR-4520 / DBT-3313 combo because there often is a wonderful synergy between Denon machines that are constructed to play together as a team. Certainly one could argue that's nothing more than clever marketing but I think there's more to it. I never had any issues whatsoever when I used my old Denon 2500BT blu-ray player with my receiver, and it was beautifully built (but too big and slow, compared to the newer Oppo). The two most interesting features about the DBT-3313 is that it offers true separation of the HDMI signal - one for video only, and a separate one for audio only (Pure Direct A/V) - the Oppo doesn't quite do it the same way - plus the benefit of having Denon Link HD for jitterfree transfer. Not sure how effective it is on bitstream signals but I've read positive feedback from owners on the improvements. Subtle, sure, but then I'm all about subtleties! Also, since it's a 'transport-player' there's no waste on built-in multichannel decoders or excessive analog circuits that you likely don't need or would ever use. Still, it's not a cheap player!
In terms of the Yamaha/Denon receiver price difference I'd say this: Yamaha is one of those brands who don't rely much on third-party components or expensive licenses (THX, Audyssey etc) as they produce alot themselves and have expertise in that area. Thus they can keep their prices down a bit.
Like I've mentioned before though, if I were to try the RX-A3020 (which does seem like a fine machine) I bet I'll just end up missing Audyssey and Dynamic EQ, in particular, since I seem to be addicted to it. Hence the Denon AVR-4520 or the processor Marantz AV8801 seem the most logical choice for me. Not to mention upgrading to Audyssey Pro, which in conjunction with MultEQ XT32 really interests me!