I'm not sure the new drain location is an issue unless I'm missing something. Seems to me a floor drain right under the tank is pretty good location. Easy enough to add elevate the sump/equipment to slope a drain line towards that floor drain, especially since you're looking at some sort of drip pan anyway.
For the ATS I would keep it separate, I'm not a huge fan/believer and with any similar type of addition best to make it as removable or adaptable as possible.
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