That drive requires cast brass Blomberg trucks as far as I know, if you want to use the Atlas side frames then you'll need an inner core to support the axles and affix the side frames.
I've not yet seen any decent brass Blombergs, they all suffer with hollow interiors and ugly bolsters that cut up and over the drive train, pretty much all after market drives are in the same vein, I actually only know of two, P&D and I think Jay Cresswell does some but I'm not that up to speed on it all. There does seem to be many ways to skin that cat, all of which require a lot of reworks, additional items and above all, $$$.
Even the OMI brass Blombergs on the GP30 I just bought are shameful when viewed low level, they are sprung axle boxes, like the ones mentioned above, the value of that is debatable in all honesty, certainly from my perspective; I've seen lots of rigid diesels run exceptionally well. The axle box springs are not to scale and just make the truck look like a toy in my eyes, other peoples mileage will vary.
The RC GP9 is designed around the Atlas/Roco drive train, it just drops right in, it's not the best, but given the price, is by far and away the most cost effective, by a massive margin.
Two other points,
gear and motor tower is quite substantial, I think you'll find whatever off the shelf drive you buy will have a high motor tower, it's the nature of the beast with these sorts of drives. Gear towers can also be quite high on the other drives, probably just below floor level but I think some are just above, Jim will be along in due course with the in's and out's as we've been batting about ideas for a true below floor drive for some time.
The gear tower height is only an issue in the cab area and then you need to decide if you need both trucks powered, do you have long grades, do you have heavy loads, if not, then why both towers. If you're just switching at slow speeds then some extra weight and one truck I would of thought would suffice, hopefully I'll get some more practical experience once the bat cave is complete.
It's easy to flip the front truck and semi hide it behind a dummy fake cabinet but only for high nose engines, of which D&RGW is certainly a user, you'll still have the drive shaft running through the cab if you want dual truck drive. The only alternative for low nose models is to cut the tower right off and make a new pivot bearing plate and fixing.
Second point,
not quite as good as I'd like, you'd need to quantify exactly what you don't like, I'm suspecting slow speed operation for switching, in which case I'd guess the trucks and gears are probably not the main issue, it'll be the motor, if you're just switching at slow speeds and not hacking along at 75 mph then your best bet is a replacement gearhead motor, add in DCC and you'll probably find running is just fine.
I wouldn't knock the Atlas/Roco drive, not given it's price and the cost of what you highlighted above, especially as you'll also need sprung cast brass trucks to go with it....same price, maybe a bit more...then add customs and excise, duty, VAT or whatever they throw at you.
The Delrin chain drive from P&D is quite popular, it's also popular in older RTR models from Weaver, I picked up a knackered RS-2 or something, right smashed up, but the wheels, gearboxes and towers are pretty much the same as the P&D set up. All up it was something like £60 from the states including all fees. You do run the risk of split gears etc but they're much cheaper to get and some places offer brass alternatives.
It really does depend where you want to go, personally I'm exploring pimping the Atlas/Roco drive far more than looking for a replacement and the inherent reworks you'll need to do to the model.
Some RC GP9 shots and notes ahead of your works.
Overall view of GP9 with stock Atlas/Roco trucks
View of chassis, the RC chassis is plastic and has a tendency to sag in the middle, there are lots of workarounds, Dave did his with I think sheet metal, I opted for brass angle, note the truck retention horns are inboard and the front one impinges into the cab.
By flipping the front truck around and reworking the drive input you can get the horns into the nose section, the inside part of the truck tower just impinges into the cab (5 mm or so if I recall correctly) so a dummy full height fake cabinet on the front wall would be needed hide it. Note, UJ is still at the front end and not flipped around.
If you want to keep the front truck powered then the UJ protrudes just above the floor, you'd need a raised centre section or whole new floor just above it, truth is with a high nose you'd probably not notice. The red line is pretty close to where the inside face of the cab front sits, that'll give you an idea of how much the flipped truck impinges into the cab area. By the same token you can see how much has been saved when the horns are flipped around, they fill most of the cab ii a stock installation.
The under frame benefits for some extra work, in my case all in Plasticard, with the knowledge and skill sets I have now, I'd go with metal and etched fabrication, in fact, I'd probably go with a whole new etched chassis and negate the need for strengthening. The flanges do split in the fish belly section as it travels across the top of the fuel tank.
The new chassis is something I hope to explore more later in the year all things being well.