There are a few things to unpack in this question, so bear with me as I go through it concept by concept.
one specific product they carry with an INCI of Cetearyl alcohol (and) Ceteareth-20. This wouldn't apply to any other emulsifier unless indicated in the data bulletin that this is the best way to use it. As it is, this method isn't advised for emulsifying wax.
I'm not sure why they're saying this should go into the water phase as we should "Treat it like the other water soluble items in your mixture." Emulsifying wax isn't water soluble - it has a hydrophilic or water loving head and a hydrophobic or water hating tail, which is how it works as an emulsifier. It connects to water at one end, oil at the other, and it creates these lovely micelles that hold the oil in little bubbles floating around in the water. I honestly I have no idea why they would suggest this. I have seen it suggested for some emulsifiers - I just wrote about adding stearamidopropyl dimethylamine to the water phase as it's more water soluble at the higher pH at which it normally exists - but never for emulsifying wax or Polawax.
Now the second part of this - why do we heat and hold the phases separately?
For an emulsification to work, we need three things - heat, mixing, and chemistry in the form of the emulsifier.
We need to use the right all-in-one emulsifier for our product - for instance, we can't use Ritamulse SCG for something with a larger than 25% oil phase - and we need to use the right amount.
We have to heat our ingredients up to the right temperature. For Polawax, it's suggested we heat to 70˚C, while the new conditioner I'm using Varisoft EQ65 wants to be heated to 75˚C. It's all about getting all the ingredients melted properly. Something like stearic acid has a melting point of 69˚C, so we heat our products to above that to ensure it'll be completely liquid.
We heat and hold separately because we're trying to make it easier for the ingredients to come together. The best way I heard it described is like this: Oil and water don't want to mix, and we're forcing them to come together by heating and mixing and using an emulsifier. If we heat and hold all the ingredients together, our emulsifier is trying to create an emulsion at lower temperatures as everything heats up, which means it has to work pretty hard to create an emulsion that's kinda weak and inefficient. You're also asking the other things that we need for a lotion - the mixing and the chemistry - to do more far more work, and this can lead to fails.
You may have to add more emulsifier than necessary or you might have to mix longer to get that lotion to stay together. By keeping them separate and mixing them together when they reach their suggested heating point of - for instance - 70˚C, we're creating the ideal circumstance in which an emulsion can happen, which means awesome lotions!
Why heat? Chemical reactions generally speed up when heated. (Think of how much easier it is to get sugar to melt in a hot cup of tea versus a cup of ice water.)
Chemical reactions also require a certain amount of energy to happen, and in the case of a lotion, the energy is the heat that's applied. Think of something like deep frying chips in a pan. If we heat the oil to 200˚F and add the potatoes, nothing happens. If we heat it to 350˚F, we get lovely crisp chips. I know lotion making isn't like making chips, but the concept is the same: If we wait until the optimal moment to combine our ingredients, we get a better result.
theory of phase inversion, which is all about the getting the temperature to a certain point so the emulsifiers create a water-in-oil lotion first, then cool down to make an oil-in-water lotion, which makes the lotion more stable. (I'll refer you to the post for more information there.)
Related post: Why do we heat and hold separately?
So the short answer is that yes, I have heard of this technique, it's not advised as it can lead to using more emulsifier than you need and unstable lotions. I know some people have had great successes with it, but it's not something I'd recommend when making a lotion in two phases is barely more work than this method.
I have to add one more thing. The author of the linked post states, "Almost each time I hear of someone having trouble with lotions I find they use the phases method for heating and mixing." Again, I'm baffled. I would argue that at least 50% of the lotion fails I hear about are those in which there was no heating and holding.