I don't know who limits the dives down here to 45 minutes but I have a guess. Most of us run one hour dives times.
...try another. There is no shortage of dive boats here in Key Largo.
In my experience in general, preselected dive times are designed to ensure that the boat can keep to a certain schedule. It has to be back at the dock in time for the next scheduled group to board and head out. Your gas pressure, body temperature, or other factors are not relevant.
For the diving in the Keys, that limit is pretty severe. The operators I have used there have longer required times, and they don't put a DM in the water.
The last dive I had in the keys, we were all given a required time, which was, as Captain Larry suggests, an hour. Frankly, that was enough to explore that shallow area. Everyone got back on the boat, we started to break down the gear, and the skipper took a roll call. Two divers were missing. We all finished packing up our gear as all the other boats in the vicinity packed up and headed out. The two divers were still missing. Anxiety began to build as we scanned the surface for signs. After more anxious minutes, someone yelled "bubbles!" and a DM donned snorkeling gear and headed out. He free dived down and told them to come up. When they got on board, we learned they had no time measuring devices, either computers or watches. They seemed blissfully oblivious to the fact that everyone else on the boat was fully packed up and ready to go when they boarded.
Most of us could have done the dive as long as they had, but we respected the given time limit because it was reasonable.
On the other hand...
Years ago I vacationed in Grand Cayman, and I made the rookie mistake of using the dive operator located at my hotel without doing any checking. I arrived in the morning and did an afternoon dive. The DM said it would be a led dive, and it would be 35 minutes long. It was. I got on the boat with 1400 PSI. I called around and found a diver operator nearby who gave us better dives and better bottom times. The next closest operator was one of the best I have ever encountered, and I would have found that out with a simply online check that would have revealed their numerous awards.
A time limit on a dive for reasons of scheduling is perhaps not totally fair, but it can be reasonable. A diver operator in the Keys who is giving you 40 minute bottom times is cheating you. Go somewhere else. When you use operators in the future, take the time to scout them out and find one who will allow you to get the kinds of dives you want. Scroll down to the regional travel section of Scuba Board and ask a few questions. It will be well worth it.