I do not understand this rant. If you have the vagues pretensions of being an actual software engineer, and your file format isn't brain-dead simple, the way to parse it tokenize->grammar based parser->ast binding phase. ASTs are simple recursive data structures, if you handle them correctly, it doesn't matter if they contain 50 or 5000 nodes or how they nest, as long as the code is correct.

SSA is a nice ish format for representing program code, but it's not the only choice and may or may not be appropriate for your domain. For example, if your language describes data instead of control flow, imo SSA is a bad choice.

I have done this and if you take care to do things right, you won't need to bother with these hacky corner cases.