There are some downsides to running in-floor cleaning. It generally requires an oversized pump. Plumbing in Solar can be a lot more troublesome if you don't plan for it ahead of time.
My advice, if you do go for in-floor. 1) you still want regular returns (maybe deep returns of you want to do solar.) 2) you still want a dedicated vacuum port. 3) You may want to consider a second pump to run the in-floor. 4) Take a look at the diagrams on powermat.com for systems with Solar and in-floor. Even if you don't plan to do solar, you never know when you might want to in the future.
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