tadapīti paramāṇūnāṃ vivekenālakṣaṇaṃ yat tadakāraṇam, paramāṇugatanīlādyagrahaṇasyānyato 'pi niścayotpatteḥ
"That too" means that the non-perception of atoms through differentiation is not the cause [of our not perceiving blue etc. in atoms], because certainty about the non-apprehension of blue etc. as belonging to atoms can arise from other [sources] as well.