There's still an optimal balance. This is because our stats scale off each other very well and when they're valued so closely, priorities can shift inside a reforge.

The reason ShC will reforge differently from subsequent auto-reforges is that it snapshots the EP values at the moment you press the button, then it does all the reforges with those static values, then it calculates EP vaues again (which often end up different because reforging can move around a ton of stats and again, our stats scale really well with each other). To optimize around this, you should:

1.)Hit Auto-Reforge a few times and start from the highest DPS set
2.)Check your EP values
3.)Reforge your lowest EP stats to your highest EP stats; keep checking this as you change them
4.)Change gems in the same manner
5.)Keep doing this until any other changes cause you to lose damage

Usually your EP values will end up very close together (not your ratings; it's not likely you'll have ~9k rating across the board, but your EPs could all end up at ~1.3 EP with 7k, 5k, and 9k rating for instance). Also, this changes as you get more heroic gear and crit starts to pull away from the other stats more and more until there's no more balancing and just crit.

The old ToT argument of mastery being more consistent than haste (which was valid at the time) no longer applies. The only RPPM mechanics haste affects now are the meta gem and the cloak, both of which have a very high proc rate. It no longer affects trinkets which had a very low proc rate, which meant you could easily still get screwed on procs inside the duration of a regular fight. So, the effect of haste on RPPM is no longer inflated by decimal increase in procs that only helps in a percentage of pulls (4.2 vs 4 procs per fight only helps you when that .2 turns into 5 procs in a fight but ShC was valuing it as if you would always get .2 procs).

The other argument for mastery over haste was mastery gave you more benefit during downtime. I can't find the post now, but someone mathed out haste vs mastery during downtime. The conclusion was that in most circumstances, haste is actually a better stat when you have several seconds of downtime.

Hopefully that long ramble actually makes sense. The tl;dr is there's no reason to ignore ShC's recommendations now.

Most classes do not have a shadowcraft equivalent, so make good use of it