The reason they're so slow is because they'll be using the Byfleet Curve to go on to the Waterloo to Reading line (via Chertsey, Addlestone, Staines and Richmond - ie round the houses) to ensure the diverted HSTs don't hold up mainline services.
You are confusing cause and effect there, I think.
1. HSTs are only cleared for platforms 17, 18 and 19 at Waterloo.
2. The obvious route into those platforms is from the Windsor side lines.
3. HSTs were already cleared between Staines and Waterloo.
4. They have recently been cleared from Basingstoke to Staines, because of existing points 1 to 3.
So although it's fair to say they won't hold up mainline services, at least east of Byfleet Jn, they were never going to go that way anyway.