Instead of TODO, I often add a NOTE instead now, e.g.:

   NOTE: Attempting to re-synchronize here would cause an infinite loop because...

This prefix distinguishes such info from normal comments, which exclusively pertain to the code-as-written.

Agreed but that's not quite what's being discussed here.

Notes are great but the context is to make a note about something that can be improved in the future (something actionable), hence it being a TODO.

Huh, if I add a TODO to typical code then it's something that ideally needs to be done there (e.g. "todo handle errors from invalid inputs" -- it'll work if you don't but... it's not ideal), or in LaTeX reports it's something that needs to be resolved still before shipping to the customer (e.g. "todo set \endDate variable"). Never is it a design decision or documenting my thought process. Why would that ever be labeled todo or, if you mean that todos indirectly convey that, why would having todos throughout the code as a means of conveying design decisions be "great documentation"?

"This information is often completely lost in issues" - of course, because an "issue" is "a vital or unsettled matter" and are not meant to be revisited once resolved. Writing design decisions or thought processes in issues seems equally weird to using TODOs to document that. They're kept around because it costs nothing and you might want to refer back to it for details on some past problem, but I've never heard of that being considered documentation.