Core level bridge and tuners on the 594! Even if the tuners are not locking they are very good at doing their job.
And the whole veneer vs real maple cap. Personally i prefer the s2 594 line.
Both the SE and S2 have a 'Solid' Maple cap - the only difference is that the SE also has a Veneer on top to 'look' prettier where as the S2 is the 'natural' grain of the top - still a nice piece of Maple, but its not the same visual patterning as you'd expect from a 'Core' which is where the 'veneer' on the SE is closer to emulating.
That's one of those 'Compromises' I talked about - whether the 'thickness' of the Maple Cap matters, the way its carved and even whether the 'grain' pattern matters because those affect the cost in both materials and labour which is why they 'compromised' here to make S2's and SE's 'more' affordable than their Core versions.
With an S2, you can (usually) see the wood, its grain and how many pieces were used in its construction - but an SE is generally covered with opaque paints and veneers to hide joins and plain looking woods that wouldn't 'resemble' the Cores they are supposed to look like. Again that's one of those Compromises to make a 'PRS Core' like guitar to sell at around a quarter of the price. When you get to S2's, you get to see the woods its made from but they are maybe a bit less 'figured' and more 'basic' design to reduce the amount of waste, therefore more 'product' from same Raw material and less labour time to reduce the overall cost vs a Core so there are some 'compromises' there too. You have to decide whether its still 'good enough' for the Money or whether you really need to spend more to get the guitar where fewer Compromises have been made to sell those models at that price.
You can argue that Single Piece necks vs Scarf Joint made from a Plank is not a 'compromise' as a player, doesn't affect tone, playability, aesthetics etc but it certainly affects the 'price' - much more 'Raw' material needed, more time taken to ensure it doesn't warp/twist as you remove material, more care needed during manufacture etc so that really affects the Price. Therefore, paying 'more' for Prettier, thicker Maple caps with more 'complex' Carve and single piece necks maybe would NOT be worth paying double for so those 'Compromises' that had to be made to make an S2 version at half the Price of a core may well not seem like much of a compromise, if any to you and its better 'value' to buy the S2 and upgrade any 'SE' grade parts. An SE owner may think their SE is certainly as 'good' if not better than the S2 or Core version for a Quarter of the Price because the 'compromises' made still produced a Fantastic instrument for less than $1k and S2's, Cores etc don't offer enough 'extra' to justify spending more on. For some, they would rather have an instrument with 'no' compromises and why they'll buy the Core. Those little differences add up to them to 'justify' that tier. For you, maybe the sweet spot is the S2, another may feel that SE's offer a better bang for buck and you are paying more for things that don't really matter - at least in their opinion.
Still comes down to personal preference and all the veneer does on the SE Custom is to create the 'look' of the Core but it still has a Maple Cap under that Veneer. Its not like the thickness of the maple on SE's is just 'wafer' thin and on S2's, you actually get a decent maple cap on it...