Mekanism sets a newly crafted machine's side configuration (items, fluids, gases, energy, ...) to pre-defined values (the sides are already set to do stuff). Might I suggest making machines not to this, as having the sides not be configured and the player having to do the configuration from scratch is better in my opinion.

Do you mean adding profiles so that all machines don't have side configurations?

If that means that a machine's sides are pre-configured to already to stuff, then yes