I can only guess, I am neither a LLVM nor a MSVC dev.
1. Compile times: If you have one file with 7000 LOC that and change one function in that file, the rebuild is slower than if you had 7 files with 1000 LOC instead.
2. Maintainability: Instead of putting a lot of code into one file, you put the code in multiple files for better maintainability. IIRC LLVM was FOSS from the beginning, so making it easy for lots of people to make many small contributions is important. I guess .NET was conceived as being internal to MS, so less people overall, but newcomers probably were assigned to a team for onboarding and then contributing to the project as part of that team. With other words: At MS you can call up the person or team responsible for that 10000 LOC monstrosity; but if all you got is a bunch of names with e-mail addresses pulled from the commit log, you might be in for a bad time.
3. Generated code: I don't know if either commit generated code into the repository. That can skew these numbers as well.
4. Header files can be a wild card, as it depends on how their written. Some people/projects just put the signatures in there and not too much details, others put the whole essays as docs for each {class, method, function, global} in there, making them huge.
For the record, by your stats .NET has 1180 LOC per file and LLVM 391 on average. That doesn't say a lot, the median would probably be better, or even a percentile graph. Broken down by type (header/definition vs. implementation). You might find that the distribution is similar and a few large outliers skew it (especially generated code). Or when looking at more, big projects you might find that these two are outliers. I can't say anything definite, and from an engineering perspective I think neither is "suspicious" or even bad.
My gut feeling says 700 would be a number I'd expect for a large project.