How to fix the bridges?

Simply put:
-Bridge pylons never work, they just end where the base model ends
-How do I fix this?

Basically, you can't, as that is how the model is modelled/designed - to have piers that only go to a certain height/depth (presumedly to save on modelling time and texture load). A lot of older legacy bridges from the early days of Trainz are like that. It could also be bridges like that are only meant for crossing shallower water or gaps of shorter heights.

All you can do is either swap it for a bridge which has pylons of 'infinite' height (that will disappear into the landscape no matter the height/depth), or, failing that, manually position scenery pylons as 'foundations' up to the bottom ends of each pylon (or clip a tall one through them to hide them). I've done this with a number of similar bridges on my routes and although it's time consuming it is worth it, especially when the bridge is perfect for the location otherwise but has no alternative with taller pylons.

You can use rail bridge supports as well.

Position a piece of invisible track under the floating supports then add in your track bridge supports.

You might have to adjust the height a little bit to ensure the bridge still isn't floating, but the good news is the all the new bridge supports get adjusted at once.