I have a case that starts at a certain stage and can either end at that stage (approve/reject) or jump to any of the other numbers stages. The sequence of stages for the life of a case is dynamic in other words. Does it still make sense to even use stages/steps? It is nice I suppose to see checkmarks on the stages that the case has already gone through. But it seems to me stages were meant to sequential relatively speaking. I don't see that these are alternate stages at all as they are not the exception. Just depends on business rules which stage should be hit first and which should be the next one and so on. So do stages/steps make sense in this case?
Looks to me such scenarios do not have straight answers. I think you should aim for a balance on what is convinient regarding the proces logic and clarity of the visualistion.
If all of the stages are optional after the first one and the sequence is not set i would consider defining those as alternative stages. You wont see the entire lifecycle at the start of the case but yeah that cycle is not clear anyways.
The advantage i see if using (alternate)stages is that changing between them is easy and more clear in comparison with using tickets to jump from one point in a flow to another.
I guess starting with stages either alternative or regular is the easiest most straightforward way. Its going to need some trial and error to uncover what the best balance is in your scenario.
In case the logic/proces involves something that is a meaningfull part of the business process then i would prefer using a (alternate)stage because it visualises the business process. If its more technical and not so recognisable by the end (business) user i would be more inclined to hide it in a process flow as it will not make the case lifecycle more clear.
For example in a project i worked in we used a "Initialisation" stage for setting up a case hierarchy, i am not fond of that aproach as the stage does not describe the business process and such logic can as easily be done just in the start flow of the case.
Looking at your profile, it seems you are new to Pega platform. If you have the opertunity i think you would benefit from the System architect training courses. Case design is part of that training.