File transform in F#

I think all three versions are perfectly fine, idiomatic code that F# experts would write.

I generally prefer writing code using built-in language features (like for loops and if conditions) if they let me solve the problem I have. These are imperative, but I think using them is a good idea when the API requires imperative code (like outFile.WriteLine). As you mentioned - you started with this version (and I would do the same).

Using higher-order functions is nice too - although I would probably do that only if I wanted to write data transformation and get a new sequence or list of lines - this would be handy if you were using File.WriteAllLines instead of writing lines one-by-one. Although, that could be also done by simply wrapping your second version with sequence expression:

let transformed = 
    seq { for line in File.ReadLines(inFile) -> Regex.Replace(line, "\t",",") }
File.WriteAllLines(outFilePath, transformed) 

I do not think there is any objective reason to prefer one of the versions. My personal stylistic preference is to use for and refactor to sequence expressions (if needed), but others will likely disagree.