upgrading components on replacement? Is it practical (or is there any reason not to) upgrade components on a bicycle when they are replaced?  For instance, I've got a 10 speed cassette on a tour bike that needs to be replaced.  The bike is mostly Tiagra components, but is there any reason (other than cost, but in this case it seems like it's only about a $35 difference) to not upgrade to 105 or Ultegra?  (Staying within the same 10 speed part.) Are there certain components that have to be replaced as a set if I upgrade?

I have looked at this compatibility chart, and if I understand it, it is saying that an Ultegra ST-6700 is a drop-in replacement for a Tiagra ST-4600.  But I'm not sure if that is everything I have to look at, can I just do a drop in replacement of any component in any box?

I'm also concerned about whether there could be other issues with mis-matched components, for instance will a better component in one place lose some of its benefits or be degraded by a lower grade component that it interacts with?
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".