Thats hardly re-engineering the engine is it?
I would call a different bore, piston size, inlet manifold, TB and ECU differently engineered.
It's hardly bolt-ons from the Ripspeed catalogue, now is it?
The main block and head are pretty much the same, as you said they have just tweaked the tb/manifold.
The head casting is the same...the block is not.
The 2.9 has a different bore.
They may may be 'pretty much the same'...but are fendamentally different, in that the 2.9 has a larger bore.
The TB and manifold isn't a 'tweak' as such. It's a different design completely.
Bigger plenumn on the inlet manifold upper (lower is the same) and a completely different TB casting (although the plate size is the same).
Thats a pretty good gain in real terms for that sort of work.
Just proves that a 2.8 can be tuned easily.
In my experience of tuning them, a 2.8 with a re-map and C VR6 TB and upper inlet manifold will give C VR6 power - around late 180s-190 BHP.
Chip a C VR6 and you gain a few more, above that though.
Port the C VR6 TB and you can pick up another couple of genuine BHP, same with a modified airbos with decent filter - NOT an induction kit!
The Golf TB is terrible and not possible to port out...just fit a C VR6 one.
The 2.8/2.9 can be tuned to 195ish BHP easily with OEM parts, modified OEM parts or basic bolt-ons...but after that, it's expensive and difficult.
Adding 10BHP to a 2.8 is easy...and cheap.
The next 20 BHP will cost you £4000.
The 20 BHP after that, probably another £4000-£6000.
Out of interest, how much have spent on your 16v to get it to 190bhp+?
I have no idea...I dare not add it up.
8 years worth of work...and around £3000 to get to the headline figures...another £4000 making it capable of using it every day and handle properly. Probably more if I really did into it. It's hard to put a price on custom made parts.
Is it likely to be reliable in the long term? 
Utterly...
Rev limit is only the same as the early ABFs anyway (give or take a 100 RPM or so) at 7300, and with a considerably lightened set of internals, it'll spin at that all day on good oil. (Synta Gold).
Nothing magical about getting the power either...just fitting the best parts you test and fing to work.
2.0 ABF, lightweight flywheel, Blysenstein Big Valve Head (1/2mm larger valves), titanium retainers, lightweight lifters, re-worked and re-profiled TB, match ported inlet manifold, match ported and opened up downpipe and exhaust manifold, 100 cell high flow Cat, Supersprint exhaust, Schrick 268 in/std ex cams, bespoke re-map. 196 BHP on the dyno it made 151 BHP on when I bought it, with around 160 lb-ft of torque.
CDA gearbox ratios with low FD, Quaife diff, 312 front brakes (Black Diamond discs, mintex M1155 pads), Koni coilovers, Eibach ARBs, Poly bushes, aggressive geometry settings. Standard Anni wheels.