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.
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.