Is it counterintuitive to build Thornmail then a Warden's Mail item?

Nah.

The damage Thornmail deals isn't high enough to warrant trying to maximize it by not building Randuins/Frozen Heart.

Thornmail is more built for it's massive amount of armor. It's special effect is kinda negligible. But Riot is experimenting with changes to it.

The damage reflection is based off of damage before reduction and the attack speed slow, well, the guy attacking you won't kill himself as fast but he will have his DPS cut which means you get to survive longer, it evens itself out