There is this myth going around that making the pony part of your gas-planning is "evil". Quite the opposite, in fact depending on your configuration it is either a must or simply more efficient.
I think it started as a way to quell the notion that you can breathe down your main tank to nothing, then switch to the pony and ascend. That's certainly not the way to do it for reasons obvious, but the answer is not disregarding the gas in your pony either.
If your setup includes a total of 2 second stages, as opposed to 3 (I see no benefit in a rig with 3 seconds, but it's personal preference), then you simply MUST have half your total rock-bottom reserve in the pony. That means your usable gas in the main tank just went up by half your rock-bottom. If you don't use it then you are just ignoring perfectly usable gas on your back.
If you have 3 seconds, then you don't have to do this - however once again you are simply ignoring perfectly usable gas and unnecessarily limiting your bottom time, if you are gas limited.
Yes, I agree it's a bigger problem with newbies to see the pony as an extension of their backgas, but I don't think we have to go to the opposite extreme and tell them to ignore the pony in their gas plan. That's just bad advice. In fact, if you carry this idea to its logical conclusion in an admittedly not-so-common scenario, with a sufficiently large cylinder like an AL40 where you would generally have a lot more gas than half your rock bottom, there is no problem with incorporating that gas into your gas plan as bottom gas either.