It all depends on the type of guitar. Some guitars - like Strats and Teles, have a wide range of saddle adjustment, so bridge placement is far less crucial. On a wrap-over bridge like you've got, there is far less adjustment available.
I really don't like using the two intonation screws if at all possible as I want the bridge being pulled tight against the posts so that it's not just pivoting on the two screws. A lot of wrap-over bridges have a much bigger gap between the locating lugs on the bridge posts than the one on your kit (which is very snug), so the whole bridge pivots forwards if the bridge isn't being pulled against the posts.
I have no idea exactly how the factory makes the kits, but I suspect that there is a lot of manual work involved with routers and templates, rather than using all CNC machines (which should guarantee identical results each time). And sometimes I think the templates aren't put in exactly the right place. The often slightly wonky holes on 6-in-line headstocks show this.
If you didn't have a flame maple veneer top, then I (and others) might suggest plugging and then re-drilling the post holes. Fine if you want a solid colour to cover everything up, but too obvious with a clear or translucent finish.
One other option (and one that I'd implement if it was my kit) is to replace the kit bridge with a wrap-over bridge with individually adjustable saddles. This would allow you to intonate each string correctly, and not have the slight compromise that a pre-set intonation bridge gives. Upgrading a kit with your own selection of parts is what makes kit guitars so interesting. But you still might not get the saddles far enough further forwards to not have to do anything with the neck position.
A few people here have used the Gotoh 510B bridge and this looks like it might be a possible solution as it looks like the saddles sit a lot further forwards of the posts than the standard kit bridge.
https://www.realparts.com.au/gotoh-5...idge-gold.html
It's a fairly hefty investment to make though (especially compared to the kit price). You'd also have to check that the 11.3mm dia. post supports would fit your existing post holes. There are other, cheaper, adjustable saddle wrap-over bridges out there, but they may not have the advantages that this one provides.
