I have a wide plank fir floor to install in July. I've done lot's of installing, but have never finished. The customers want it to be stained a dark, chocolate brown, and we have yet to decide on a finish. I'm trying to push OSMO oil, because it is very simple to use.
The reason I've never done it personally is because the clients have always done it themselves. If they go with something like a water based, I'm going to farm it out. This house is south facing with big windows, and is 100 ft from the lake.

1. Should I spray the stain with an HVLP system (which I have), or just use a brush and rag?

2. Are water based finishes much more expensive than the oil?

3. What are some alternative finishing products I may not have heard of?

Will this flooring be already sanded ready for finishing? And it's fir? I've done many fir floors before and always thought they looked best in a natural. It let's their golden and pink colors come out nicely. Why anyone would want to stain it dark brown is beyond me. Just put a walnut floor in if you want a brown floor. That's my opinion. But to your questions.
1) I don't know about spaying on stain or finishes. Perhaps if you did it before installing but us finishers typically roll, pad, mop, rag or buff on stain. Same with the finishes.
2) Yes. They can cost 5 times as much. $20.00 per gallon for for OMU and as much as $100.00 a gallon for Bona Traffic. But the big box stores carry some inexpensive ones for less. There's Flecto Varathane Diamond Finish, Park's Water based, and I think Minwax and Deft also have some single component water-based finishes. These are single component and not as durable or scuff resistant as professional water based floor finishes.
3) Carlisle Restoration, who has been manufacturing wide plank flooring for decades, is a big proponent of WaterLox. I've used this finish and can tell you there isn't anything easier to apply. I'd recommend this finish on that fir floor. This finish can be top-coated with a polyurethane at a later date or after ample dry tim.
https://www.waterlox.com/default.aspx