Yes, an auto shop is going to have all the equipment available to them to spray your guitar and could even very likely use the same finish since there is likely already paint / primer on it. Not like they'll be spraying directly on wood. If it is a repaint and they use Eurothane or something like it, they'll likely need to prime so there is no reaction to the existing finish.
Edit:
While auto finishes are expensive, they're also the most durable you'll find.
They come in every possible color, solid and metallic that you can imagine, they'll have stacks of books showing chips as samples.
I'd suggest going with a base/clear finish, it'll stand up to abuse much better than a single stage paint. Chips will be in the clear rather than the color coat. Also with a clear coat you can put your stickers on the base before the clear and have them sealed in forever.
A big body shop will have their own paint mixing equipment and if they don't they can (mix or) order as little as a pint at a time so it shouldn't be too expensive.
Be sure to have them tape up anything you don't want finish built up on. If you're going with a base/clear solution you could build up a good bit of finish when you consider primer etc. Knobs, pick-ups, switches, and where the neck bolts to the body.
Oh, and you'll be able to wax it.
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