I have done it both ways with big block mopars, but my last few I've been using Permatex Ultra Black on the sides with success. It does depend on the RMS retainer you're using. Some aftermarket units use two thin rubber seals. Those channels would be too hard to fill with RTV from the top. My most recent build was a Ford FE Big Block which has the same type of side seal / pin system (as the topic starter pictured) and I again filled the void with the Ultra Black. It works very well.

The trick is using the supplied screw on applicator that comes with the Permatex. You get the nose of the applicator in side the void and squeeze hard filling the void completely. I use one of the intended rubber side seals to push the Ultra Black down and pack it in the void. Then I top it off until it's oozing out the top and wipe flush.

Ultra Black takes a while to dry when thick, so I recommend letting it set up for a few days before adding oil / starting the engine.