is there any way to use telegram's own export output
Telegram Desktop can export to JSON so it just a matter of importing these JSON files. It does slow down when needed but can export 1k chats in minutes if you don't export media.
> The other way is actually risking your account being taken down for flooding the API.
Have you heard about such problems? Are there published API limits?
I don't use Telegram so much, but for what it's worth I know people who used Chatistics to export 10s of thousands of messages without a problem.