Here's your answer:
Change the line thickness! ;-)
Yes, I read your post asking that I don't say that. But aside from my contrarian nature, I've got a good reason to say it.
On Layer 1, build your silkscreen outline. Use 8 mils, 10 mils, whatever you like, don't worry about part size, make it pretty.
On Layer 19, build an actual size (maximum for all alternate parts) part outline. Use a 1 mil line width. This one is for assembly drawings, output to IDF. It must be a single closed polygon.
On Layer 20, copy the Layer 19 shape (1 mil), and if you need additional clearance around the part for pick and place or ICT considerations, add it here.
Set the Body to Body clearance rule to whatever you need, run your Verify Design with all outline layers except Layer 20 turned off. Now here's the trick: set up your Clearance Checking to check Placement Outline, not Body to Body (that's right, it doesn't really make sense).
Setting a 20 mil clearance, placing parts with 1 mil outlines 20 mils apart will give you no violation. Less than 20, you'll get a violation. My tall parts are oversized by 60 mils around the perimeter, that gives me 80 mils clearance.
Layer 20 is the key. PADS understands that as the Placement Outline layer. When placing with DRC on, PADS will use Layer 20 to determine legal Placement Clearance.
I have renamed Layers 19 and 20 in my default settings as "3D Outlines" and "Placement Courtyard" respectively.
Can you show some images, it will help me to understand and clarify your problem.