This will be an interesting read. On another thread, I wrote about my concerns about weight, weight distribution and GVWR. As you've already noted, lots of people put a lot of weight up top. Many will also state "never had a problem" but this doesn't mean it's right or safe. You have already assessed your set-up identified the weakest link. My ARE CX HD that has an internal frame that connects to two load bars through the canopy and it's rated for 550lbs dynamic. I chose this because it was the strongest system with the highest load rating I could find for a canopy. I'm surprised you were able to get a rating from ARE for a regular top as most of the canopy manufacturers don't tell. My guess is that the 300lb you quote is the total dynamic load for your topper but the Yakima bars are only 75lb each (very typical), totaling 150lb dynamic, on pavement, x 0.75 for off road, so 113lb in the dirt. The 250lb RTT is already over the pavement rating and over twice the off road rating.
I have no doubt that there are safety factors built in to the load ratings and some other considerations. It would not surprise me that with your current set-up, your canopy roof may start to show cracks in the gelcoat where the racks are mounted. How many clamps per side holding the canopy down? If only two, I'd definitely add a third. I would suggest adding a third load bar, taking the dynamic, pavement bar rating up to 225lb; still not 250lb but getting closer.
I just peeked at Yakima's website and a truck bed setup with two bars; rated for 165lbs, "weight limit" (whatever this means) and under the suggested "basecamp" use it recommends only small and medium RTTs; a typical medium RTT is around 150-160lbs.
Good luck.
