Slow upload and download speed on raspberry pi

No this shows that multi-threading is working (1.0 load is 100% of 1 core). Honestly, perhaps it’s just a function in php that uses 100% CPU for some reason, this would be the first point to check. In this case, there wouldn’t be any issue of your setup.
To exclude influence of your setup, you could 1) try on a 32 bit system if that changes anything, 2) try a setup with nginx (then you have the separate php-fpm processes). But it’s quite some work to do this.