Can I keep chillies in alcohol long term without continuing to affect the flavour?
The hotter the pepper, the shorter the infusion time, and the less time for the tequila to pick up any unwanted green vegetal flavor the thick skin of a jalapeño can impart (serious eats)

For presentation you could possibly get away with one nice-looking, thin-skinned (and not too hot) red chilli in the bottle, after straining the tequila off the real habañeros.  I'd give this a go (or even make 3 small bottles: strained; unstrained; strained with decorative chilli) it if it was for drinking myself, but for a gift I'd probably either:


say it's for drinking soon, or
decorate the outside of the bottle with a couple of nice-looking dried chillies tied on.


I have found that in some infused spirits, leaving the fruit in too long can cause unwanted flavours (e.g. rhubarb, which picked up just the vegetable flavour my link warns about) while in others you can leave it as long as you like (e.g. blackcurrant).