The limits for lifepo4 chemistry are 2.0V bottom and 3.65 Top, so yes it does damage your cells in some way. Possibly shortening cell life. Most case scenario lithium batteries would like better to be discharged above 2.0V limit and charged without hitting top limit. This way you will get more cycles out of them.
I had some spare time to think about the "P" setup requested. It is an early draft, but sharing anyways. It should come out little more costly as i would need to use pure copper for outside clamps as current will flow between paralleled cells in series. End terminal blocks as well out of copper, as 2P, 4P will allow to pull tons of current.
Here is 2P6S setup:
2P6S board size is 78x160mm compared to 48x160mm in 6S configuration
End terminals would come out through protective plate and The Builder would have a choice to drill it where he needs it, the size he needs it to be and trim it