David you've asked a great question and I'm certain you'd get differing opinions even among renowned hybridizers. That leads to what I'd say is the first point to keep in mind-- there is not necessarily any one correct way to hybridize or make hybridizing decisions.
Secondly, the factors specific to each individual hybridizer, like goals and program size, will vary greatly and make a significant difference as well. For example, the approach of a hybridizer growing 200 seedlings a year will most likely be different from one growing 10,000. And hybridizers will vary in exactly how much of a priority they place on traits such as scape branching-- and that will effect their approach.
Thirdly, even the specific daylilies and seedlings you work with will provide variability that may or may not fit with what has worked for other hybridizers. For example, you may happen to be working with some daylilies that pass on great scape or plant habit more easily than most. Sometimes even with one hybridizer's program there can be great variability. For example, one particular seedling might resist being given a face-lift while most others do not.
Therefore one answer would be that you may just have to try things out for yourself and see what works for you in your specific situation. To a certain extent this is simply unavoidable.
However, by asking the question you very reasonably are seeing if you can save yourself some time and grief in that process. My recommendation would be to take into account all advice you can get from seasoned hybridizers, but perhaps give a bit more emphasis to ones who are working in a program more similar in size to your own.
My program is probably similar to yours so I'll share some thoughts:
You have to define your assessment of traits, and establish your prioritization of traits. While they can change with time a bit, you need to know for example just exactly how YOU define great branching and how important it is to YOU. Once your priorities are established, stick with them in your decision-making process.
Having said that, a hybridizer with a small program will out of necessity occasionally have to lower their standards a bit. It is not always practical to demand perfection when you don't grow enough seedlings to likely get there. So letting the occasional pretty face with less than ideal scapes stay as a bridge plant may be OK-- if the pretty face really is worth it. The key is being tough about which pretty face is really worth it. Too many exceptions and the whole hybridizing program can severely weaken.
I do find that in general improving bloom features is easier than improving scape and plant habit. I am more likely to keep a great plant that isn't quite there with the bloom than the other way around. I will make an exception if I am trying for a very unique and hard-to-get bloom feature. In that case, especially in a small hybridizing program, I have no choice but to get the bloom feature and then try to improve the plant. But if I'm not trying to blaze a radically new trail, I'll prioritize the plant.
However, I must add that I usually don't keep a great plant just because it's a great plant. To me, there has to be something "promising", some compelling feature to the bloom.
I also am in zone 5 and I was a bit surprised to find that, more often than not, the seedlings that end up having great scapes make that apparent right away. Even if they aren't 5-way in their first year of bloom, they almost always are clearly superior to their siblings right from the first year. Very rarely do I find it takes four years to know which ones are the great ones.
These are my casual thoughts at this time...