First Issue:

So far, I've only tested this with Normal Quarry shape card and Void Quarry shape card. But even when I select an area to quarry with either card, the builder will not quarry the nine blocks below it, despite the blocks being selected. I am unsure if this is intentional. This ONLY happens if the builder is directly placed above the platform

Second Issue:

Support blocks will stay even when support mode in the builder is disabled, requiring me to get rid of them by hand. While a minor nuisance, this could be a big problem for people building or quarrying much larger areas, where getting rid of them by hand is simply too much extra work.

RFTools Version: 7.61
Minecraft Version: 1.12.2
Forge Version: 14.23.5.2779
McJtyLib Version: 3.1.1

EDIT: I checked curseforge, and I speculate this is because McJtyLib was last updated when the last version of RFTools was released. However, I am forced to use McJtyLib 3.1.1 for version 7.61, even though it came out around the time the last version of RFTools did. Correct me if I'm wrong.

The Builder avoids the blocks directly around it (to prevent problems with the builder accidentally mining itself).

Latest of McJtyLib + RFTools should work. People are using that combination a lot.

The issue with the support blocks not always disappearing is known. BTW, right clicking them will remove a lot of them at once.