Getting great stereo sound from multi channel sys.

IMO, you need to answer an important question (or two or three) before you choose from your options:

Do you plan to use your subwoofer(s) for stereo listening?

If you do plan to use them, Option 1 may not be your best choice. IME, AVRs and Pre-Pros will likely get you substantially better subwoofer integration than you'll achieve with a traditional stereo preamp. "Likely" is the key word there, as absolutes are risky, but the bass management systems in pre-pros and AVRs really do this job well.

A second question runs to source material. If your music is strictly digital, the trade-offs of DSP are IMO pretty beneficial. Not everyone here will agree, but IMO crossing in the digital domain and room correction schemes like Audyssey are simply a better mousetrap. If you use mainly LPs or other analog sources, the decision is more complicated. If you're amenable to subjecting your analog signal to processing in the digital domain, you may still prefer options 2 or 3. If that idea troubles you, I'd agree that Option 1 is best.

As to Option 2 vs Option 3, good AVRs are probably better value, but a pre-pro and separate amps may be preferable, particularly if your main speakers present a difficult load to an amp (provided that your budget allows).

"If you do plan to use them, Option 1 may not be your best choice. IME, AVRs and Pre-Pros will likely get you substantially better subwoofer integration than you'll achieve with a traditional stereo preamp. "Likely" is the key word there, as absolutes are risky, but the bass management systems in pre-pros and AVRs really do this job well."

The OP's preference is pretty strong for 2 channel. Going with theater gear just to integrate a sub probably wouldn't be worth it for the hit you will most certainly take in overall SQ. It may be a little more work, but you can get a sub working well without all the processing. For a system like this, a sub made for music would probably be a better choice. Or maybe just use the sub for theater only.

Thanks for all of your help! Any model recommendations for integrateds or preamps with HT bypasses?

There are integrateds with HT bypass available from many manufacturers - Marantz, Musical Fidelity, Creek, Arcam, Krell, are a few that come to mind. There are 2 channel preamps from Musical Fidelity, Parasound, and even Rogue if you want to consider tube gear.

Any specific model recommendations would be based on your budget and the power demands of your L/R main speakers. Since you mention that your thinking about the Triton Twos, these are fairly efficient at 8 Ohms and 91 Dbw. That would further widen the range of models that you can consider.

I find it a bit curious that those endorsing option 1 are not also commenting on the op's choice of speakers. The GoldenEars seem to me to be an odd choice for someone who wants to maximize 2 channel stereo performance.