The Plant Factory trees I use do not have a 4 season cycle (though they change color in the Fall months). I found this out when I set my route to December and all all of the trees went back to Summer green colors. The ones I used to use had full season (green, fall colors, bare branches in Winter), but they were so poorly optimized that it would cause major FPS drops for me. Draw distance in both the main settings and in the route settings doesn't matter. LODs (level of detail) may not be present in the trees you are using. If they are it may be set really low.
Also at full distance (22,000 in the main settings and disabled in the route) PF trees now won't load until I am extremely close Fly a couple of inches away and they look like butt.. Perhaps the recent patch nerfed them, but I just replaced the offending trees with others I have.
When I used to play LSPD:FD (the police mod for GTAV), some police cars would disappear (as they drove off) and only the police men would be visible. The fix was setting a graduated LOD (100, 200, 300, 400, 500, 500), but in Trainz being what it is, high LODs can cause more problem in FPS.
If your issues are caused by meshes, then I'd remove those trees and find something else. Sucks I know, but appearance is everything to route builders. I've made many compromises as a route builder because I am a bit nuts with perfection, and flaw is unacceptable so I find replacements then use them.
This can happen with some other types of assets that were poorly made (many are very recent), but again Trainz is not doing things under the hood as it probably should.