I've made an alternative Assets Manager. This Assets Manager regenerates the files ONLY if the files have changed since the last time they were compiled, thus eliminating overhead. It is compatible with Cssmin and Jsmin from Phalcon, so it's still very fast since those minifications happen in C.
https://github.com/Swader/bitfalls_utils/blob/master/Bitfalls/Utilities/AssetsManager.php
I haven't added the whole thing to composer yet, but the Asset Manager itself is in use on all 17 of my Phalcon sites (autosusados.hn and derivates, look at links near bottom) and it works like a charm.