Does this completely override a normal language file or does it use a normal language file and then apply the changes listed on top?

It lets you create own new filetype, based on built-in lexers(highlighting) and parsers(symbols).

Is the documentation there simply out of date?

It's in the regular filetypes documentation.

What am I missing out on with a custom filetype compared to an actual language file?

For something as simple as assembly, probably not much. If the assembly dialect had weird syntax (compared to "traditional" assembly) then some stuff might be mis-highlighted or show up wrong in the symbols sidebar.

The alternative is to write your own lexer in C++ and own tag parser in C and integrate it into the 3 related projects (Scintilla, Ctags and Geany).

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