I've got a Gen3 3sgte. I was wondering what difference does an aftermarket turbo manifold make in terms of performance over the stock manifold?

So just the manifold and nothing else changed? Bugger all.

Basically I have a high flow ct20b running around 17psi on high boost. I've got some modifications but in relation to this area its basically an aftermarket turbo manifold with tuned length pipes, high flow ct20b and full exhaust system. Now one of my primary pipes on the manifold runs very close to the silicone turbo joiner and at the track, like Calder 2 weeks ago, it ends up causing the silicone joiner to burst (due to heat) so I was considering running the factory manifold if there won't be a performance drop. So basically want to know if there will be a drop?

Doubt there would be. I'd stick with a standard manifold

Stock manifold would work well for you as you can use the factory heat shield. The manifold I think you might have just creates a lot of heat in the engine bay and possibly lowers performance.

I have a self made heat shield in place that vents out all the heat. Have a raised rear hood and extractor fan but its just the one primary pipe that is the issue. When does a stock 3sgte gen 3 start spooling and fully spool at 13psi?

Unless you get a $1000+ ($2000 with the way the Aussie dollar is) on a well made manifold, don't change it. I had a cheaper aftermarket manifold (not done through a high performance specialist). Cracked three times, extra heat to the engine bay. Taking it out and replacing back to stock was the best thing.
Port matched the stock manifold (suppose to help flow by not having ridges on the joining but no data to prove or difference noticed). Makes basic sense to port match (remove cast edges in the joint) or get it professionally done if you want to throw money at it and they will port match and flow test for a better result (however is tiny difference from what I understand).
Boost level does not equal power is what I have learnt. Reducing engine intake temps, air flow efficiency, correct fuel supply, tuning tuning tuning makes the big difference. Look to supporting mods before pushing boost, 17psi does not automatically equal more power than 7psi if not supported/tuned for it.

Those Ebay stainless specials are a complete liability, as not only do they take up more space, but foul with the stock hotpipe and cause more heat issues than the stock item.  The stock manifold is more than capable of dealing with a high-pressure CT20 and is bulletproof.  Sure, it's not pretty, but you are building a track car, not a show queen, LOL
 
Oh, and those stainless ones are notorious for cracking :)

Yeah I heard that about the ebay ones. This isn't an ebay special from the look of it, hasn't cracked and on the track and is glowing red hot. I would actually like to keep it if it didn't cause an issue with my silicone joiner. I'm happy with my engine package as it is power wise and spool, its just the head heat going to the joiner that is causing my issue. I know the stock one wont cause an issue but I'm not sure if there is a performance drop, never had the stock one. When does a stock Gen 3 start spooling and when does it hit full boost at 13psi?

Circa-3000rpm.