I've actually been thinking of raising the par to 100. This would involve making 5 more away matches par 3s. Only the top 8 would remain par 1s away (7 matches).
I don't think you need to change anything Prof. 90 points is the threshold to "guarantee" top spot, as no team has finished 2nd with that number of points (although it could change this season).
And although some teams muck up their own Par 1 / Par 3 status, it's still the same for all teams competing at the top of the table. So if Burnley are poor for the whole season, then they're poor for everyone, and visa versa for Watford.
The joy of the APLT is it's simplicity. Otherwise you're gonna need to look at isolated periods of form (how do you deal with Burnley being crap whilst they were in Europe, but hitting their stride once they go 1 game per week?), or some teams having a hex over others (like Chelsea over Spurs, until last season). It'll just get too messy.
In short ... I'm happy the way it is at the moment, and the way it's always been. It was a brilliant concept from the start. Thanks for all of your work on it, Prof.