It does look like it could be an optical illusion from the angle the pic is taken. Looking at the nut, it appears that both E strings are the same distance from the outside edges of the nut. If the nut is perfectly fitted, both strings should be the same distance from the edge of the fretboard. If the nut is the issue, they can close up the 'gap' between each string and leave a bigger gap at either end of the nut. May make it a bit tight for the strings for fingering.
By zooming in at the full pic, the 'e' string at the PU end of the fretboard actually looks further from the edge than the 'E' string. Again, this could just be the optical illusion from the angle the Pic is taken.
As for the price, the fact its the 'most' expensive, and the 'expectation' of the quality that you get with a PRS, that is negated by the fact that this is no longer relevant with a 2nd hand guitar. There is no way this is new at that price and therefore could have had the nut replaced and cut wrong, the frets could be 'worn' in a way that causes the 'e' to slip off (have you checked either of these) or even the way you play which may suit a 'strat' or wider neck. I am NOT saying its your play style at all, just that it could be a cause or part of it if its a combination of all of these.
Do you have a ruler or gauge to measure the distance from the edge of the Nut to the E string, the gap between E-A, A-D, D-G, G-B, B-e and finally e to the other edge of the nut? All of these measurements should indicate if or where any issues are. If these don't show any issues, you can check the Frets, see if they are evenly as high across the fret top to bottom. It maybe that the bottom (the 'e' side') could be lower than the top ('E' side), slope off to the edge of the fretboard. If these are 'evenly' sloped, they can still appear level from Left to Right (22nd fret to the 1st fret). If the 'plain' (G. B, e strings) had cut a groove into the fret, the previous owner may have been overly aggressive in sanding the lower side to get rid of the dents and levelled them left to right and not bothered to level them from top to bottom as well.
You really don't know the history or the competence of any previous owner(s) or person that may have worked on this guitar through its life. The reason it was up for sale may well be because the previous owner messed with it to sell rather than pay for a professional re-fret and new nut cut. That can cost a LOT compared to the 'value' of the guitar. That may have cost £300+ and not added any 'extra' value to its sale price. Sell for £725 and pocket the lot or spend £300+ and only pocket ~£400...
You cannot blame PRS or expect a 2nd hand guitar to be representative of the brand. Had you bought it new, then you perhaps could apportion some blame to the manufacturer - although they only check it before it leaves the factory. Its in the hands of Distributors who will send them to retailers, who may put them out on display for anyone to come in play. It may well be checked and set-up by the store when its purchased. For 2nd hand guitars, you have to factor in any changes, set-up's to their preference, even possibly replacing the hardware and then returning to stock for selling as they want to keep their after market PU's for their newer guitar. There could be more than 1 previous owner too. Any of these can affect the 'quality' of the instrument since it left PRS.
Its certainly not a brand new guitar - that's cheaper than the RRP for an SE Custom. You really don't know the history, how its been treated, how competent the previous owner or any person that may have done 'work' on the instrument prior to you buying. As I said, the previous owner may well of 'cleaned' the guitar up and been too aggressive with fret levelling, may have replaced the nut themselves etc to sell. Selling a guitar with frets that have string dents in them isn't going to sell for that price and its very expensive for a re-fret. Its a bit like cleaning your car inside an out to make it look better to get a higher price - even though the clutch or something is knackered and really needs replacing...
If you have luthier measuring devices to actually check, maybe take it to a professional and get them to check and assess it - its difficult for us with only a couple of pics to go on.
