I recently just brought my first Inferno Tower and placed it in my main base. prior to this i had already created a Clan War base and when i was nearing 5 mil to get my tower i altered it to where i would place it.
After placing it at my main base i went to alter my Clan War Base layout and noticed there was a little red house icon in the corner. i recognized it from when i initially designed the base when i had yet to place my Town Hall or Clan Castle. since the new design had a hole in the "non-deploy-able" area which the Inferno Tower would fix i placed it in there anyway.
I know that Buildings and Upgrades are not carried over to a Clan War Base if they are completed after Preparation Day so i have opted out of Clan Wars for the time being (as the Inferno Tower wouldn't show up until it's done and attacks could use this hole). however given this Clan War Base is my only one which i selected to use, had i not placed my currently in construction Inferno Tower into my Clan War Base and i entered into the Clan War would that layout would it have been used? if not would mt regular base have been used?