Go figure. When someone finds something neat to do with a machine, the developer decides it's too powerful and takes it upon them selves to nerf it for everyone instead of LEAVING IT UP TO THE SERVER ADMINS TO DECIDE IF IT'S TOO POWERFUL!!!!
While the Mining well machine is MUCH faster than a quarry, it's also more difficult to get set up and requires more resources to make. So yes, you can mine a path 16 blocks wide, 4000 blocks long in about 32 IRL hours (If running at full speed) with the Mining well machine while it takes the better part of a day for a quarry to mine a 60x60 area, the mining well machine is already more expensive to make and use than the Quarry even without making it a pig.
For the Quarry, you craft the quarry, mark your area with landmarks, plop it down, give it a place to send the blocks, give it power and voila! you're quarrying...
For the Mining well Quarry machine, I'll give you mine as an example... I have 5 Redstone Energy Cells, two energy tesseracts, something like 32 redstone energy conduits, 16 Wireless Mining Turtles, 16 Mining Wells, 16 relays, frames, tube frames, panels, a cover, two frame motors, a battery Box, seven solar panels (Bluetricity solar panels), a chunk loader, a computer, two wireless redstone receivers, and a portal frame. Back at my base, I have two Energy Tesseracts being fed by two energy bridges generating the MJ power to run it full speed. They were originally being powered by a bunch of UHSP's, but I have now migrated over to a self sustaining fusion reactor. The mining wells actually suck power out of the redstone cells faster than the tesseracts can send it over, but enough is being sent that they fill back up during the pause between he turtles picking up the wells and the frame machine moving. With the little over 400MJ/t that the 16 wells draw at full speed, 5 energy cells are pretty much required in order for the wells to run at full speed. before I had the energy bridges, I was running it off of 16 Electrical engines which couldn't even come close to keeping up, so I had to shut the machine down after 20 minutes or so and let the energy cells recharge.
And to be able to cope with the volume of stuff coming out of one of the frame miners, you need a fairly robust sorting and storage system. I started with a ton of barrels, some of them inter dimensional, a redpower tube network, a sorting machine and several 'overflow' diamond chests. That worked very well. I've since upgraded to an AE network, and automated my ore processing with 8 industrial grinders, and I store the dust until I need ingots, since some recipes call for dust.
This is NOT something you're going to make the first day you're on a server... You will need to do a bunch of quarrying just to be able to get the resources to make the frame machine. In my case, I run the frame machine in a waterless mystcraft world that I created specifically for it.