The companion guide states that:
The machinist is limited to creating automatons with HD no more than twice his
class level and with a number of special abilities no greater than
his class level.
I had a question of interpretation. When calculating special abilities does one count all positive special abilities that have been sunk into the automaton or only the number of special abilities that remain on balance after restrictions have been added. So for instance, if a first level character takes the personal automaton proficiency allowing for a personal automaton of up to 7000 gold and the character bases his design upon the Ornithopter example from the class.
If it has 1 HD, excludes the standard immunities, keeps the default movement rate, adds flying (+1), adds hover (+1), add passenger capacity (+1), removes attack (-1), and requires operator (-1). +1, +1, +1, -1, -1 = 1
This would fall within the 7k gold amount the proficiency provides. However, is the number of powers that count against the mechanist’s level calculated at the end, here 1, or is it the total number of beneficial abilities given regardless of detractions added to reduce cost and time, here 3.