I think my biggest concern is actually how it would affect resale value.
Good point. Plenty of people, myself included, would walk away if there's the slightest issue on the HPI so I wouldn't be surprised if you have trouble selling it on.
I know it's exciting to get your first bike and hard to walk away from what looks like a nice, well looked after bike, but honestly as atpbx said there's plenty out there they will pass HPI without a problem so you wouldn't need to give it second thoughts.
If I was buying my first big bike I'd also struggle to walk away from this despite a failed HPI check and would also look for reasons why it isn't dodgy. I know what it's like
[Edit]
Also, as far as security goes, I'd recommend a decent disc lock for when you take it out. Light, easy to carry, quick to put on and can survive a simple cropping attack because there's nowhere to grip on it. Granted it won't help if they lift it into a van, but it'll certainly stop or deter wheeling it away. If you have something solid you can lock it to (at work or wherever) then get a chain.
Wait, you're friends with loads of mods. Are you a spy? ¬.¬