Then following common sense, all via points should be in turn instructions (named or not).
(we cannot bend the common rules as we like for only some cases)
Also have you seen how shaping points (or via points) are used in other routers?
(we should not try to reinvent the wheel)
Shaping points:
Shaping points are a big advantage when you not only give the route types and avoid types for the routing but if you force the routing to use prefered must visit segments in your route. Sometimes you have to set some shaping points to reach this. And then the decent marking is a big advantage when showing the route.
Via points:
To be friendly to other statements: This could be the solution. Because all nonamed Via points you don’t want at turn instructions can be replaced by Shaping points.
I agree with @WalterG
For me this would be OK:
But configurable whether shaping points are taken into account when rerouting or not. (Or always take them into account)
Shaping points still differ from via points as follows:
What makes clear differences to via points.
Nevertheless, it would be important to be able to take shaping points into account for rerouting (configurable or always).
For example, you can create POIs or planned breaks as via points, see them clearly on the route and receive turn instructions for them.
Sections that you want to drive through, but which are not necessarily defined by a certain geographical point, but define an important section of the route, can be defined by shaping points.
Just my suggestion …
The thing is that first implementation was as described by @WalterG:
(then users complained for imports, etc. and we started the changes…)
The desires of the users at the end not always allow us to work economical. Sometimes we spend time for work with not so useful features.
But introducing the shaping points and your first implementation is a big gain for the app. To differ named and unnamed via points for turn instructions was a (little?) unnecessary detour. But at the end drawing the right conclusions makes the app better!
When the shaping points and the named via points are available in the published version of the app users will recognize the advantages. Some earlier desires loose priority and perhaps investing time to it is unnecessary.
IIRC the issue was, that coordinates were exported into the name field.
I think this is solved now on the website: Website: Export and waypoint names - #21 by boldtrn.
If it’s necessary, I could review the whole process completely from the beginning. 
This also could be solved in the app by implementing a button “unname all waypoints” or a button “convert all waypoints to shaping points”.
off topic:
@devemux86: thought about implementing a PayPal-Donate-Button for your PayPal account?
Already available in waypoints list:
Add shaping points
The route is built by shaping points
added on map:
Add via points
Via points are places you want to go through when navigating the route - the voice navigation will notify you of them and in case of route recalculation the via points are not detoured.
Hmm …
“in case of route recalculation the via points are not detoured”
Does this mean, that Locus treats via points different than shaping points?!
It seems to handle them differently in voice guidance (as is the case with other routers).
Or your question is specifically about rerouting?
My question is specifically about rerouting.
Basically Locus has two routing options:
Point priority - Locus recalculates the route to the nearest transit (or ‘via’) point on the planned route. If there are no ‘via’ points, it recalculates the route to the final point.
Route priority - used when you deviate from the original line and want to get back to it - Locus navigates you to the original line as soon as possible and on the nearest place - the line (route) matters.
But both options could lead to skipping waypoints.
So why do they say:
“in case of route recalculation the via points are not detoured” 
Anyways, just thinking.
But Kuviger could do better 
Fully support this statement! I plan my routes always with about 3-4 Stops (routing points) but about 15-20 shaping points (yes I like the proposals of kurviger but I still use also the old map for planning). Skipping of shaping points due to detour recalculation makes sharping points function useless for me.
We cannot add more options. Already the “Waypoints in instructions” option seems unnecessary.
(and adds severe maintenance problems)
We must finalize the workflow with some sane defaults, like most routers work and users expect.
So the only needed change seems to be that shaping points must participate in rerouting,
even if they are before the next via point. Does everything else work the way we need it?
Well, this is then different as proposed above:
here and here
If you don’t want to have different rerouting strategies (strict for via points, flexible for shaping points)
than, the only difference (between via points an shaping points) would be:
Shaping points:
Probably easier to implement 
Well, we cannot fill the app with options that will make its maintenance impossible.
But we must examine other routers, participate in discussion and make 1 decision.
this would be OK for me