One of my players asked the above and the text isn't very clear. Reading the Improving Aptitudes section on p. 152 of the core seems to indicate as such.
1 Answer
Bonuses from cyberware and the other external (in relation to the character) sources apply after the morph-imposed maximums.
Eclipse Phase core rulebook, p124, Aptitude Maximums:
Some implants, gear, psi, and other factors may modify a character’s natural aptitudes. These augmented values may exceed a morph’s aptitude maximums, as they represent external factors boosting the morph’s ability. No aptitude, however, augmented or not, may ever exceed a value of 40.