I understand where you're coming from, and it's a question we've seen come up quite a few times.
The main reason is that Pure is listed under Rust's Community servers, which are governed quite heavily by Facepunch's Community Server rules. Because of those restrictions, we can't add gameplay features that alter the vanilla experience, such as raidable NPC bases or other modded PvE content. Custom maps and monuments, like Waffle House, are permitted under those rules, which is why you'll occasionally see custom map additions while the gameplay itself remains vanilla.
If we were to add features like raidable bases to Pure, it would no longer qualify as a Community server and would have to move into the Modded category.
That said, we do offer many of the features you're looking for on our modded servers. From what you've described, I think Elysium would probably be the best fit. It includes custom NPCs at monuments, roaming train and convoy events that you can raid, and a much more challenging PvE experience overall, while still giving you plenty of opportunities to learn combat and base defensefrom the NPCS before jumping into PvP.
We know those types of features are popular, and we'd love to offer them on Pure if the rules allowed it. Unfortunately, that's a limitation set by Facepunch rather than a decision made by us.