With so little time you might be best flying into Heron and leaving Cairns until you have time to explore the fascinating hinterland.

As a general rule there are fewer species as one moves away from the equator on coral reefs. Heron however is particularly diverse from all reports (I've not been there). You will still want to take a boat out at Heron to get to some of the other reefs but the option to dive in whenever you feel like it sound right up your alley.

Don't even think about driving Brisbane to Gladstone. It's at least 6 hours, with some notoriously dangerous stretches.
IMO Heron is great, as long as you like birds. There will be thousands of terns nesting all over the island in November.
If you can put up with that then there is lots to do and see on and around Heron.

I've been Heron several times (most recently 2001) and several times out to the reef from other places like Port Douglas and Mackay. If you stay on Heron for a few days you'll see a LOT more than you would on a day trip out to the reef from the mainland.

In the lagoon (the area of the reef exposed at low tide, accessible from the beach), you'll see rays, turtles, shovel nosed rays, maybe the odd harmless reef shark. And patches of coral and colorful fish.

The reef edge, where the reef emerges from the sea floor is the best place for coral - miles of it, all sorts of it. If you're a good swimmer you can snorkel out to the reef edge from shore - maybe a couple of hundred yards away from the beach at the closest point. But it's better to take one of the snorkel boats out to the reef edge (at a price of course). It's a 5-15 minute ride. Often they'll let you drift snorkel over the coral for a mile or so, if the tide is right. Besides coral, you'll see all kinds of fish and maybe some big things like turtles, reef sharks, and manta rays.

Yes there are differences between the southern reef and the northern reef, but they are not that striking and they shouldn't really come into play.

I've done the drive up from Brisbane every time I've been to Heron. I never thought it was that bad. You could also consider a stop along the way such as a couple of days on Fraser Island - totally different to Heron.

I love Heron Island, I would highly recommend it, but you do need to like birds. In nesting season there are a LOT of them.

I would fly from Brisbane to Gladstone to take the ferry out to the Island. It takes about 45 minutes. Gladstone is an ugly mining town, I wouldn't recommend an overnight there.

November is the time of the synchronised mass spawning! See below from the monthly calendar for Heron Island:

"November: Turtle egg laying begins, Wedge-tailed Shearwaters nesting begins, Black Noddies eggs can be seen in the nest. Average rainfall 54.1mm Average temperature min 18.5C max 29.0C Average water temperature min 22.0C max 28.5C The annual synchronised mass spawning."

I did a trip where we did both, reef trip from Port Douglas and three nights on Heron Island, early November several years ago. I thought they were both wonderful, but there was definitely more variety of "sea creatures" at Heron than the reef trip from Port Douglas. If you have to choose, I'd pick Heron Island over the Cairns/Port Douglas trip for more time on the reef, reef walks, etc. We did both snorkeling off the beach and from the boat, and recommend doing both. You also get more time with the general reef environment. You can just watch the sharks and rays from shore, the water is so clear, and at low tide, you can walk several hundred meters out to the reef's edge with the water level below your knees.

The birds, yes, many birds. A bit of an odor, but you get used to that in a very short time and don't notice anymore. Mostly, it was the sound of the mutton birds at 3 a.m. that was the issue. Bring earplugs if a light sleeper.

I suggest you to visit Heron Island, a beautiful place to visit.