First. I'm not an expert high horse power car builder. But I did stay in a holiday Inn once. 0

Like many of us out there I read a lot and I'm a big Mustang fan.
But I didn't not say it was a "bad idea" to combine a stroker motor with a super charger. However in general, all things being equal, super chargers are normally paired with "square" motors.
Like everything in life building a fast car is a series of engineering "trade offs". Trading off factors such as:
- Horse power
- cost
- weight
- reliability
- complexity
If $$'s really aren't an issue, then select "all of the above" and build the blown stroker motor with a custom cam and ported heads, custom tune. Rock on. Don't look back.
But if $$ is important, then wouldn't it make to most sense to pick a combination that yields the most HP for the least $$'s? Don't focus too much on the specific parts and ignore the WHOLE of the combination. Remember that the motor is really part of a system.
That's why it's important to list the project goals IN ORDER. For example if cost and reliability are more important than HP that likely will affect the choices made.
I hope your "take away" from this is to rely on the real world experience of the engine builder you have chosen to do the work. After all it's their professional experience that you are paying for. Right?