I think to answer your question, first we have to see why conflicts happen, and what is the true meaning and process of merging?
Conflicts occur only when two or more developers are working on the same file at the same time and then they both try to check in. The first developer won't get any conflict, of course. But the second (third, fourth, and so on) would get conflicts. Why, because (s)he has some code which is partially or entirely different from existing code on the server.
This in nature means that the second developer has something in mind different than first developer. This difference can vary from styling, like using
new UserManager().GetUserName() instead of
UserManager userManager = new UserManager(); userManager.GetUserName(); up to the level you mentioned, which means that both developers had different ideas of how to refactor the code to improve it.
Merging, on the other hand, doesn't mean that developers can check-in their code without considering conflicts. They should and must address those conflicts. If conflicts are not important, then they may check-in and override previous code. But when they see something entirely different, they should call the previous developer, and talk to him, so that they can both get coordinated together to check-in the best solution.
For example, if you ask two developers to improve online-payment library, and their work overlap, this means that at least on some places, there are 2 different solutions. So, one of those solutions should be talked about and be accepted, thus checked-in, as the better solution.
I don't agree on preventing these circumstances, as we should tend to be more real than theoretical. Sometimes a guy is really good at CSS, while another is really good at ASP.NET Markup. But their work may conflict when they should both work on login page to make it work. I mean, if we think real (not ideal), we can see that many times this phenomenon (conflict) happens.
Another point I just wanted to mention, is to use tools to help you in your check-in process. These tools usually visualize the difference of server code and developer code, and helps a lot in determining which part should be checked-in.