cape-universal vs custom overlay

I’m getting our product ready for production… During the development phase I’ve been using cape-universal and have a script that runs at boot time that just serially runs config-pin to setup all of the 30 pins we need. There is a mix of GPIO, eQEP, i2c and some uarts… this little script isn’t exactly ideal for boot time reduction, it takes 10-12 seconds or so to run according to systemd-analyze

Will I save a bunch of time if I write this pimux’ing mess as a custom device tree overlay (no, we don’t have an identity eeprom on our interface card)?

Will a custom overlay properly setup the required directory entries in the filesystem for bonscript to work? We do some slow GPIO and uarts through bonescript, the eQEP and i2c is done directly from the PRU.