Perhaps the trick is to use thicker stock material and mill it for tighter fit, rather than tubing. There is a manifold with this slide connection made for Cummins 5.9. I have never heard of it leaking. I haven't seen the one on the BMW but might be a good option for adaption.
As for packaging, yes, this is 3" pipe feeding to LP and outlet from HP is also 3". If I choke down flow with smaller diameter pipes and valves like yours then I can package it a lot tighter. I do like the use of the flexible couplings in your manifold design.
I am running a log style manifold very similar to the design you show above on my GBT2056V/CR engine. I have not had any issues with warping and leaking and that is with a hot tune. One would think the flexible coupling you installed would alleviate most of your issues.?
imo 3' is widely too big, for reference. with a 3' exhaust on a 3.0 tdi doing 450hp/1450 kg/h you measure like under 50mbar pressure after turbine.
this is with the gas at lets say 650-700 degC and ambient pressure and lets say 4 meters pipe with some bends
If you will be able to run this kind of airlow on a 2.0, I would suspect the pressure before turbine to be around 4500 mbar abs at minimum, ok, it might be 950 degC. but the air density, and this space it requires will be ~4 times smaller.
I know the example is overly simplistic. but I think you get the point. this is why on a small displacement/high boost engine, you come away with very small intercooler piping, primary runners, throttle body, etc. the only area where you need to use NA logic for sizing is at the piping pre compressor and post turbine. any pipe that has pressurized gas in is, can be way smaller to flow same massflow at fix pressure drop
the manifold I designed was aimed to have the piping 'free' as in not used to support the wieght of either turbo. the flex joints will also live for long if you use them for what are intended, which is to compensate for thermal only expansion/movement. this kind of joint will fail soon if they have too much movement, as for example caused by engine vibrations.
I started with a 12mm plate. then after inital surfacing it was like 11mm. then after I had welded the slip joint I had to straighten it again. now its below 10mm left :/