Why a new Package update generate DRC error after waiving ?

I've redesigned a custom TO220FLAT Package

First I created a TO220shape.ssm  with PCB Editor. Then I created a surface mount T220build.pad in Padstack Editor using TO220shape.ssm. Then I created a TO220FLAT.psm in PCB Editor. I placed 3 Connect pins and 9 Mechanical pins for the TO220 TAB, using standard through-hole pads for better current handling.

Adding those Mechanical pins created many DRC errors caused by the proximity of those pads attached to the TO220shape.

Thru Pin to SMD Pin Spacing (-200.0 0.0) 5 MIL OVERLAP DEFAULT NET SPACING CONSTRAINTS Mechanical Pin "Pad50sq30d" Pin "T220build, 2"

I corrected the situation (so I though) by Waiving those DRC errors, thinking that they could not cause any problem and because that’s what I want, i.e.: 9 through-holes under the TO220 device. The idea being that when this device is mounted flat on the PCB it could carry lots of current via 9 pads that could make a good high current conductor to inner layers.

I then saved the Package and updated all related footprint schematic parts  in Capture. Created a new Netlist. Then I imported the new logic into PCB Editor to reflect that change. When the File > Import > Logic is finished I get no feedback error! (which, for me is a substantial achievement in itself)

Now, in the Design Window I see all those DRC errors popping up again, despite the fact that I waived those DRCs back in the Padstack edition. If I run a Design Rule Check (DRC) Report I will see all those DRC listed again. Now, I understand that I can go ahead and waive all those DRCs (100 in total) but I’m thinking there is got to be a better way of doing this.

Please, any advise is welcome. Thanks