Not quite sure what you're getting at. Direct HGR-STJ involves the junction off the mainline to Lewisham and the junction next to St Johns.
Exactly. It creates a conflict that isn't there. Just moving the conflicts from point a to point b doesn't help much.
When going via parks bridge to St Johns is direct and does avoid Lewisham but what happens is that the down stopping services then clash with services coming from the down kent fast and you end up always waiting at Parks Bridge to cross over to the slow. This move used to happen a lot and even with the services we have there is still a slow crawl round and wait for anything coming across or up.
The conflict coming across the diamond being moved down to the end of the North Kent still means that anything coming across the junction needs to wait at the bottom for services to cross over. This also happens already and you are often waiting for services coming across you at St Johns or services coming round from Parks Bridge.
There is only one way to get rid of the conflicts; remove them altogether. Anything up the North Kent goes to Cannon Street, anything up the Mid Kent goes to Charing Cross. It's part of the reason why the Vics got moved to the Sidcup. It removes a conflicting move across the junction at Lewisham. You could change the pathways so that each move across the diamond is paired up but the issue is that the slightest knock to the service and you conflict anyway. Not stopping the Charing Cross services at St Johns and New Cross and sending them over the flyover helps remove the conflicts.
A brief look at the train service requirements allows for some flexibility and train planning is an unenviable job. I'm not sure that playing crayonista is helpful and with Charing Cross Vs Cannon Street Vs Victoria means that you will always get a conflict somewhere unless you make a drastic sacrifice nobody is willing to make. One minute passengers want more direct services and then the want flexibility and a place to change. Some want a fast service and others demand a metro style service. Nobody wants to make the sacrifices needed to run a robust and efficient service :/