two different things

Like a lot of ‘thw~’ words, this came in to the melting pot of English from Scandinavia. In this case the root word thverr meant crossed or perverse, thence thvert, thence thwart. So the thing in common is that the bench is athwartships – across the width – whilst the verb form of thwarting an action is to place an obstacle across its path.

Ain’t language wonderful?