The KDL-55X4500 if it’s like Sony’s of that vintage I’ve encountered has good 240p handling but I’d hardly call it perfect, still plenty of issues with motion, drop shadows etc. Unfortunately no there’s nothing you can do on the OSSC, the blackout is caused by the change in refresh rate. It’s possible that things connected via SCART are all processed/frame converted to 59.94, thereby eliminating this dropout but introducing a little stutter during motion.
For horizontal shift, try changing the H.Backporch in the advanced timing menu.
You’re basically correct, in almost all cases its Rec. 601 for SD and Rec. 709 for HD.
GB Interface – Yes you will find that happens on most TVs due to the odd refresh.
Auto on the 480p sampler tries to detect what kind of signal it is, Dreamcast always reports this wrong.