Yes, more and less convenient at the same time. In different ways.
The kinds of things engineers do to our modules would require taking them apart, making huge changes to them and putting them back together. That would probably take... well, a lot longer than "beep, boop, done", even with the help of robots and maybe nanotech and stuff. Worse, it wouldn't really work very well with the modules mounted on your ship. I mean, if you want to open up your car's engine, ream out the cylinders, and slap on some customized headers, you usually pull the engine right?
So why not have Engineer mods take time? Only, because an engineer is NOT going to want to work on stuff while it's installed on your ship, and also gameplay-wise so that you can still use your ship, you store your modules, SEND them to the Engineer via the transfer system (so you don't actually have to make the trip! Unless you want to that is), and then let the Engineer work on them while you gather up materials for your next big mod. Of course you'd need to be able to send modules to a system you're not at, instead of just being able to have them brought to the system you are at like you do now.
More convenient: You don't have to personally chase engineers all over the Bubble anymore.
Less convenient: If you don't chase engineers all over the galaxy, you have to wait for the modules to get delivered, and either way you also have to wait for (insert carefully thought-out time period here) before your module is ready.
Please don't ask for more pointless time sinks, when I engineer a ship I've already sunk in the time to collect all the mats needed before I even set about getting them modded, I don't want to have to then wait an arbitrary amount of time before I can refit them.
As a sidenote, I have actually rebuilt a car engine without removing it from the car, was able to strip the block down, hone the cylinders, fit new rings, bearings and seals all without taking the block off the engine mounts in the car (granted it's not common but you can do it on some cars).