JSX was also created with the intention of using traditional conditional/looping constructs, but that hasn't stopped Solid and Preact from repurposing it for fine grained reactivity. Preact's signal implementation has Solid-like Show/For components [1].
I won't speak for the author of the proposal, but given that Lit itself has special control flow mechanisms for conditionals and loops (the cache and repeat directives respectively [2][3]), I can't imagine the proposal being too opposed to these mechanisms.
[1] https://github.com/preactjs/signals/blob/eae850a9f3aa62e505a...
[2] https://lit.dev/docs/templates/conditionals/#caching-templat...
[3] https://lit.dev/docs/templates/lists/#the-repeat-directive