Joel pushed no "methodology" in that sense at all. What I see is Kent Beck, who pushes a methodology which has taken up a religious like following in "IT" or corporate developer circles. Joel just ships software, and judges things in terms of commercial success in the market place.
I am not really a fan of Joel's advice, but if I look at the relative successes, I would have to favour Joel (also, listening to him speak now, on that podcast, indicates that in his "old age" he really has less advice, he has mellowed out and realised that there is a lot more variables at play).
I think any methodology really boils down to: have good people any they will make something work. That is the only common thread in successful projects/teams/products that I have seen (and others). Its 80% people, perhaps more. Therefore any other tweaking of things are really like premature optimisation.
And I like brain candy. Its sweet in a bitter world ;)
I think Paul Bucheit said : "Limited life experience + overgeneralisation == advice".
