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The file extension is completely irrelevant. In fact, the extraction code is common by a good 75% between JPA and ZIP. Both are simple archive formats holding unencrypted, GZipped data. Also, this kind of speed difference cannot be reproduced on any of our test and live systems, nor in the thousands of sites we have worked on over the years while helping clients. Simply put, JPA is just "ZIP light". It is the same format minus all the optional extensions, the central directory at the end of the file (itself a relic of the days where ZIP files would span several physical disks) and file checksums (because PHP is pretty bad at calculating them for large files without crashing the server). Compressing to JPA is marginally faster than ZIP, extracting from either is the same speed within statistical significance.

A speed difference of that magnitude would have only made borderline sense if you were comparing JPS (encrypted data) to ZIP or JPA (unencrypted data). The JPS format stores everything encrypted, including file metadata, in up to 64K packets. If your server uses an older processor which doesn't have AES functions at the hardware level (or PHP was compiled without the optimization that makes use of said functions) the extraction should be substantially slower. Still, 20 minutes is way too much. Something like 3' would be more like it.

The other factors that can have this orders of magnitude effect on the extraction speed is the operating system and the way the storage is attached to the computer. Windows is stupidly slower than Linux, macOS and pretty much all other UNIX-derived systems. This comes down to the inefficient way the operating system handles data transfer to the disk and the effective lack of usable disk caching. The way the storage is attached can be a bottleneck, too. An SSD connected over SATA III can reach full speed (theoretical SATA III maximum: 600M/sec; typical server-grade SSD speed: 550M/sec). An SSD connected over fiber optic may reach full speed depending on network conditions. An SSD connected through NFS over regular Gigabit Ethernet will suck as bad as a regular HDD.

Then there other factors at play which could limit throughput. Do you have enough free RAM for a healthy amount of disk cache?Ideally you would have a disk cache that's as big as the amount of data being extracted that the OS doesn't have the time to write back to the SSD while the decompression (non-file-I/O) operation takes place. Also, is there an antivirus or other daemon monitoring the file contents? That could have an orders of magnitude impact on the extraction speed.

If you consistently observe an orders of magnitude difference when accessing JPA files you should contact your host. Most likely they are running some kind of antivirus or other file monitoring daemon which puts a lock on the file, preventing PHP from being able to read from it. It wouldn't even be in my top 20 of stupid things I've seen hosts do.