If we don't lose them to a waiver claim, we won't lose them in the Rule 5 draft. What General Manager would decline to claim a player on waivers, then select that player a week later in the Rule 5 draft? Only a GM that wanted to deal with the additional constraints that come with Rule 5 selections!
There is also the possibility that the Phillies will use one of the two spots just opened yesterday to claim a player off waivers, instead of waiting for the Rule 5 draft... obviously depending on what players other clubs may have put out on waivers yesterday, to clear space on their own rosters. Those players become a part of the "available" pool, and it would be silly to wait for the Rule 5 to draft one of them if there's interest.
I don't see waiting 'til the last minute as "odd." Because it is the last minute, it makes it just a bit harder for another club to make a waiver claim - because clubs have added players in the meantime through trades, signings, etc. Moreover, if the Phils had finalized a move for a player who needed a roster spot, they could have asked waivers on Perkins or Vielma at any time, so not clearing the space earlier didn't constrain them in any way; they didn't really sacrifice any flexibility here. (It may have troubled some fans, but this GM doesn't appear to be taking marching orders from the PR office.)