some folks out there called it a scientific research vessel or somesuch, simply because they were running missions for Genesis.
Because we have since seen that torpedoes and probes are fired from the same casings, it seems to me that in star Trek, science ships pretty much can function as "destroyers/frigates", and are able to use the same designs. A ship with 4 torpedo launchers can fire several probes for studying a nebula, or fire several torpedoes in a fight. The Reliant's role is gets debated on this site, but I don't see why the design cannot be a "science-ship" (which actually makes more sense in for the plot), and also a ship with formidable weapons.
a gold box with red pinstripe.
The saucer and nacelle RCS markings all have the thruster detail but the rectangles next to the rollbar phasers do not
they are painted the darker blue-gray and the gold markings are separated
They are separated, but they are not really far apart, as they could be interconnected.
or those rectangles were just random decorations as some of the various markings are. But the placement fits the RCS placement pattern.
But the way the ship was painted is a strong indicator to me that they are NOT phasers and the gold rectangles are RCS markings
I agree that I see evidence that the yellow areas themselves are not phasers. It seems odd to have both the large blue emitters, apparently 2 smaller blue emitters, and two yellow emitters all in one place. That seems like more weapons than a starship would have, and more obvious weapons.
Since the ship has a number of other RCS exhaust points, can you provide clearer proof on how and why these fit in best as RCS thrusters? And also explain what you mean by the fact that they "match the pattern" as to where they are placed?
he gold rectangles due to their proximity to the side phaser emitters and lack of thruster detail would suggest that they are phaser-related
I think the obvious answer is being largely ignored: these details can literally just be access panels that are labeled with yellow paint and a red stripe. I once went to a museum that had military planes and there were numerous such labeled panels, some large enough for a person to enter, some small enough to cover equipment. The TOS ship had some markings that are similar.
Without the dark thruster detail, it does not seem like a thruster. Without the ball detail, it does not seem like a phaser. However, it is placed near some phaser, or warp drive, or photon torpedo, or mission-specific equipment. Why not just have an access panel to service whatever is underneath that yellow area that probably connects some important types of technology together?