Why does Lama Atisha say those "observing pure conduct" shouldn't take (some) Tantric initiations?
Verse 64 mentions the secret and wisdom initiations.

These two initiations are taken only in the context of highest yoga tantra. Therefore, the three lower tantras are not concerned here.

From the point of view of highest yoga tantra, there are two ways of achieving enlightenment: 


With an actual consort
In the bardo, after death


It is said that lama Je Tsonkhapa could have achieved enlightenment with an actual consort, but he would have to disrobe (or to ensue a defeat). Instead, he chose to achieve enlightenment in the intermediate state.

So, there are these two ways of actualizing the completion stage and upholding the secret and wisdom initiations. One them would be a defeat.

Other practices, such as the consumption of infinitesimally small dosage of alcohol, is not considered as a transgression of the pratimoksha. During Lama Chöpa Tsok, for instance, we dip our finger into alcohol and lick it. There is no practice where you consume more alcohol than that. In addition, we say that if you refuse to do it while you actually took a highest yoga tantra initiation, it is breaking your tantric commitments.