Did someone figure out how to configure exception from the pad-to-pad clearance rule for a given components or just the same components in general?
To the best of my knowledge you can't do this (and I'm not an authority on the subject) but it raises the question of why would you want such an exception. If that spacing is acceptable on one place then why not in any other place? To the best of my knowledge you could create a design rule that allows a smaller spacing for those two nets, or to allow a smaller spacing between SM pads specifically (which is perhaps the closest thing to what you really want).
Were it me I'd change the offending pads (or all of them for that matter) to rounded rectangle as per IPC recommendations.
It's standard practice to limit spacing 0.2mm to be at the edge of manufacturer's capabilities for the whole design and avoid crossed PCB on the panel, but have ICs with smaller spacing on the same design. The soft really need "pad-to-pad for the same component" rule. Limitation by nets will not work well. Additionally, it's a pain to configure 64 rules for a 64-pins IC. Indeed, spacing between SMD pads is the closest, but then DRC will not check pads of different components. I though about a workaround where I would need to draw a courtyard around each component at the distance half of what I need between pads of different components with following courtyard-to-courtyard DRC Rule, but I didn't find any suitable rule. Which rules stands for component-to-components? Courtyard is responsible for controlling spacing between components?
They don't work for that purpose. They are based on 3D models. This is, btw, wrong solution - pads can go far from components shape. Averaging is not applicable here, all components are different. For components clearance the only correct way is to check outlines or courtyards clearance. So, I guess no workaround here expect setting pad-to-pad high globally.
The test I performed was for components without 3D bodies attached and a very exaggerated courtyard top border. The DRC was definitely using this outer border when highlighting distance rule violations. However I think the system simply uses anything associated with a footprint when checking distances so it is not possible to force the use of courtyard and to ignore anything else associated with the component.