As written, the Enhanced Summoning ACF for specialist Conjurers also gives up the bonus feats.
But, a generous DM might let you take each substitution as a separate item.
1st level, swap Scribe Scroll for Augmented Summoning.
5th & 10th levels, keep the bonus feats.
Enhanced Summoning (Ex)
At 1st level, a conjurer using this variant gains the Augmented Summoning feat for free instead of the Scribe Scroll feat.
At 5th level, the conjurer's summoned creatures become particularly tough to dispel. Add 2 to the DC of any caster level check made to dispel the conjurer's summoned creatures. At 15th level, this addition to the DC increases to 4.
At 10th level, the conjurer's summoned creatures gain an additional +2 bonus to Strength and Constitution. At 20th level, these bonuses increase to +4. These bonuses stack with those granted by the Augmented Summoning feat.
A conjurer using this variant does not gain bonus feats for advancing as a wizard.