I completely understand your mentioning this location at top of your list, and as such it was always on my radar in my days. I notice a couple of other regulars on here have commented on this as well. There were those (in SW Planning circles) in BR days and continuing forward through SWT days who had an interest in this subject, and (AFAIR) plans were also submitted to higher levels, although I wasn't that close to that aspect so am unable to quote specifics.
Suffice to say, that when it came to the 10 car (SWT) suburban plans the proposals to electrify a number of sidings in Woking Up Yard for that particular project, some discussion did take place in relation to allowing space for any future flyover for the UP Portsmouth road, to come across and down in the area currently occupied by #1 & 2 Up Yard reception roads.
But as Bald Rick comments, how beneficial would such a flyover be in relation to additional paths from Woking onwards to Waterloo in todays world, and that is the crux of the matter?
In L&SWR/SR and even early BR days, it may well have had some benefit, but in todays world (being unaware of the current timetable as it is now in post covid/SWR days), I can only comment in regards to SWT days, so pre 2017, when the timetable (peak wise) was all but at its maximum capacity between Surbiton/New Malden and Waterloo on the UP (a.m. peak), therefore any more services that (might?) have benefitted from a flyover on the UP at Woking Junction, would just add to the 'timetabled' congestion Between Woking and Hampton Court Junction.
The timetable revamp of 2004 made the best use of Woking Junction (as was/is), in that UP & DOWN Portsmouth Direct services were, where ever possible, planned to cross Woking Junction at the same time, each half hour, the benefit of that being that this maximised the number of paths that would then be available to other services on the Bournemouth main line between Brookwood and Woking.