We run a similar setup in production at VideoToBe – FFmpeg inside Cloudflare Containers with R2 mounted as a local filesystem via FUSE (tigrisfs).
On the debate about Cloudflare vs Fly vs spot instances – for bursty, infrequent workloads that already use R2 for storage, Containers are a natural fit.
The container accesses R2 over Cloudflare's internal network, so files never hit the public internet.
Check out our implementation - https://videotobe.com/blog/how-we-process-video-with-cloudfl...
(The main difference is we don't use Cloudflare Queues in conjunction with Cloudflare Containers. You can set max_instances to your desired settings to process parallel requests.)