I think it's definitely planned. I understand when blues/folk performers add random beats here and there to fit the words, but that's more of a spontaneous thing which can change from performance to performance, and is usually when it's a solo performance. I do it myself when improvising solo fingerpicking pieces. However when you have a band cutting a track in the studio I'm pretty sure the structure was deliberate, even if the performances were flexible to some extent.
I hear it a lot in traditional Irish tunes, especially when there's a vocal. However, when a band takes a traditional song and turns it into an arrangement for multiple musicians, they still sometimes throw those "random" extra beats in, only they're not so random. It's a way of giving an ensemble performance a more authentic, organic feeling. Take P Stands For Paddy as recorded by Planxty, plenty of extra beats thrown in, but it's obvious they've practiced the bejesus out of that arrangement.
But it still throws me, and I have a hard time counting it, especially in a tune like this where the bass line is so familiar yet throws you that curve ball. I often wonder whether it sounds odd to me simply because I have a musical mind which looks out for this stuff, whereas if you never think about music theory, it mind sound totally natural. Another example is Blackwaterside by Bert Jansch, I transcribed it years ago and it took me ages to get my head around all the bars of different length. But I remember playing it for a non-musical friend and asked him whether he found anything weird about the rhythm...he said he didn't.