Custom Page Templates is offering containers in which Dorico can Lay-out music, and how Dorico fills these containers regarding the options in layout-options.
I agree with @Lillie_Harris , that as I mentioned having multiple flows is better achieved via layout options, than via a page template. Also, if we knew this was your goal from the beginning, we would’ve advised you strongly into this direction way earlier.
There is a lot Dorico does for the user, and it’s usually best to let Dorico have the upper hand there, except for when you really know what you are doing. (And still then Dorico keeps the upper hand, you just nudge it a little).
Maybe let me also share some examples of what custom master pages can do, besides the general layout of first and standard pages, where the design choices are more clear maybe.
First: Program Notes with music examples. Why a custom master page? Because you want to be able to quickly apply it to scores and parts of a piece (in this case orchestra). All the scores and parts can use the same master page while simultaneously differing significantly in layout options, especially page format(!), but also other things such as staff size or note spacing.
Second: pages with only text but no music, again as a front matter. That means, a custom
Master pages doesn’t need to contain a music frame and will this push the music just further back, again possible to be used in different layouts:
Third: changes in layout for a single page only. This can be used if for example you need footnotes on only one page and thus don’t need a frame for it on all other pages. Or in this case, I added another chapter headline above the flow, it’s from my opera. #9 is a normal flow header, but with #10 starts the third chapter of the opera and thus I added the headline to a variant of the default page template, which lived within the same page template set.
There are obviously many more use cases, but having multiple flows on one page is something dorico handles natively in layout options and creating page templates for that is this unnecessary, which means page templates are not (normally) used for this kind of layout change.