Jackson Auto Machine is very reputable, well equipped and experienced shop I wouldn't have problems to trust even with my own block. Either they exaggerated or you misinterpreted them, but there's a little truth to every of their claims. Putting 95 pistons (or any but the OEM 7.8:1 pistons for that matter) no big rods without having the crank counterweight/piston + rod combo ratio brought back to OEM specs and rebalancing the crank in the process may be, in fact, less reliable than the original OEM configuration. There's a reason why one shouldn't be running the butcher and randomly knife-edged cranks on the street or just bolting any kind of rods with any kind of pistons to the stock crank since the counterweights of the crank weren't designed randomly either - and their mass was calculated and matched to the specific piston + rod combos. Of course, no one ever bothers to take the fact even to consideration while wondering why his built block didn't last. It also pays off to have the oil passage plugs of the crank pulled and clean all the crap that accumulated in there for the past 14 years.
As for the balance shafts removal, they're there to help to cancel the harmonic frequences of the engine as well as reduce the natural vibrations of the rotating assembly associated with every I-4. Removing the balance shafts may promote material fatigue of the components of the rotating assembly, but those issues are rarely associated with our engines (although cases of cranks split in half, thrown rods and shattered flywheels are well known and documented). Although utilizing smaller and lighter rotating assembly, the Mirage block doesn't use the balance shafts straight from the factory while being very similar in construction to our blocks - which could be used as an argument in favour of the balance shafts removal in our blocks as well.
As for acidikjuice's budget and expectations, $600 won't get you too far and many corners will have to be cut, which may result in decreased reliability of the engine. If you want to build a reliable race engine, hot-tanking, magnafluxing and sonic-testing the block is just the start. Weight-matching the rods and pistons while assigning them to individual cylinders during blueprinting and prepping the crank is not cheap. Any monkey can slap together a 4-banger in less than an hour, but there's a huge difference between building a POS street engine that will not survive 20K miles without crankwalking or throwing a rod and top-of-the-line reliable race engine. Of course, not everyone wants or can afford some mega-buck beast that will support 900 HP, but one should be aware of the fact that the more corners he cuts, the less reliable the rebuilt engine is going to be - especially if mixing components that weren't designed to work together in the first place. Can you have the 95 pistons put on the big 6-bolt rods, the block machined and the rotating assembly assembled for $600? Most likely yes, but one can also spend just a couple of hundred bucks for some cheap junk tires, Maaco paint job or listen to the stock radio through the stock speakers. There's nothing wrong with that and it's obvious that if you're using the cheap TopLine rebuild kit and only consider hot-tanking the block, the reliability and performance of the engine aren't the highest priorities and requirements you're after. In that aspect, having the block torque-plate honed or Jackson Auto Machine do the work would be unecessary overkill. The engine you're building might not be the most bad-ass wonder ever built or last for ever, but it'll do for some mildly moded street car on a tight budget.