upgrading components on replacement?
There's no harm in doing so, as long as you identify compatible components.

You do take a hit on cost, by which I mean that components work out a lot cheaper when bought as part of the bike, rather than standalone. So economically it would probably make sense to stuff the money in a piggy bank, and save up for a new bike with better components, since when that time comes you'll get more bang for your buck. But if your pocket is willing to take that hit, go for it.

I haven't looked at your specific case but in general, upgrading from something Shimano to something Shimano will work, as long as both mechs have the same number of gears on the cassette. 6700, for example, is a 10-speed system so as long as 4600 is also 10-speed, you should be safe.

The other caveat to bear in mind (when upgrading brakes/shifters) is that a couple of Shimano mechs have different pull ratios to others. In fact, there was a question about this just a couple of days ago which I remember links to a document explaining what mechs are affected.

Lastly, while I start by saying there's no harm, there might also be no gain either. That's going to depend on you, and on the rest of the bike. So you're right to raise this in your question, but it will result in "no gain" rather than "harm".