I've been working on doing similar with containerized dababase servers for testing, while still having versioned scripts for prod (multiple separate deployments).
In the early stages of development of whatever the ETL process is, I keep the database and just empty it out each time. As I got more of a sense of what I needed, I started DROPing my TABLEs more often and remaking them. Eventually I would make the whole database from scratch once I was along the way and had most everything fleshed out.
Do you anticipate hitting a wall at some point where the total time becomes a problem?
No, the time never grew significantly.
For one of the analysis projects, just one step of the analysis was quite time consuming but it would have been that way no matter what. SQLite allowed me to let it grind away overnight (or even over a weekend) on a workstation without tormenting production servers.