Can someone elaborate on the limitations bit?

"Little Snitch for Linux is built for privacy, not security, and that distinction matters. The macOS version can make stronger guarantees because it can have more complexity. On Linux, the foundation is eBPF, which is powerful but bounded: it has strict limits on storage size and program complexity. Under heavy traffic, cache tables can overflow, which makes it impossible to reliably tie every network packet to a process or a DNS name. And reconstructing which hostname was originally looked up for a given IP address requires heuristics rather than certainty. The macOS version uses deep packet inspection to do this more reliably. That's not an option here."

Is this a limitation of the eBPF implementation? Pardon my ignorance, I'm genuinely curious about this.

eBPF limits the size of the code, its complexity and how data can be stored. You cannot just implement any algorithm in eBPF for that reason.

That's not only a weakness, it's also a strength of eBPF. This way it can provide security and safety guarantees on the code loaded into the kernel.