If your racks are different sizes, then you need to have a different thermostat for each of them. The different lengths/sizes of heat tape is what is likely causing the different temperatures. Until you correct this, you're going to keep having temperature issues, which are potentially very dangerous, between them.
As far as a night drop goes, there's usually no reason. Many (most?) don't even do it during breeding season anymore. I still do, but I feel like I'm one of the exceptions around here.
Finally, the answer to where to take temps is "it depends". For your hot spot, you want the temp of the floor (below the substrate) directly above your heat source. That is the hottest location in your enclosure and the goal is to make it safe if/when they decide to lay there. For the rest of the enclosure, it is less important where you take the temperature, as it's the ambient temperature you're measuring there.
I hope this helps!
Best regards,
Eric
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