Similar to the way there are more and more mutant animals as time progresses, potentially more and more plants can mutate as well. Both being reflective of the gradual alienation of the environment and further pushing the difficult in acquiring said resources.
Much like how the Poppy plant is already mutated, further along the game calendar trees and plants can start developing initial or advance mutations such as:
Thicker bark (more energy to cut down trees)
Thorns and bards (interactions has a chance of hurting players unless properly protected)
Side effects or toxicity/poison (for edible berries or others)
Grappling vines (grabs players that try to go past it)
Thicker vegetation (grass or other vegetation could grow in large proportions, thus slowing player movement or obstructing your vision)
Merging woods ( Trees merging together to make a thick wooded wall, preventing passage unless removed) Inspired by Darkwoods.
Sentient and aggressive crops ( Similar to a triffid, except these would come in the variations of crop plants that have become sentient, and likely aggressive to players)
And potentially so much more to an ever evolving yet ever dangerous world.
Also think about mutations that might possibly be benificial to humans in some way. Things like plants that turn into extreme bioaccumilators that collect heavy metals. They become extemely toxic in the process but can also be used as a source for those same metals. Trees that turn into into some sort of land coral and are thus very difficult to cut down or destroy but could also be a huge source of limestone. Huge mutated flowers that usually eat insects and function like a trap but where (toxin-free) nactar can be collected from. Various canivorous plants that you can actually collect the seeds from and plant yourself to use as traps or a fast growing plant with very nasty poisinous spines that can be used as a part of fortifications. Not to mention that many normal ponsinous plant can be used for things like poison arrows I don´t see why mutant plants would be any different.
There would be two visions of how you could make living off the land more difficult/make wilderness areas more difficult as the game progresses. These would be to as you suggest to make more dead and toxic biomes with not much in them or the route that is presented in this threat which is that the doesn´t collapse and starts to mutate thus making life much more dangerous to the player. Personally I like the second option more as it simply add much more content in terms of gameplay and interesting content than simply turning more and more of the map into comparitivelly boring dead zones.
I do however like the idea of smaller dead/warped biomes for thematic effect things like a locally warped inviroment as the aftermath of the large portal storm or even as part of a local spacial anomoly. Things like deadzones that expant to a certain point could also be cool surounding things like hazards waste and dump sites. Implying that something that wasn´t meant to be there was thrown in it or things wheren´t properly disposed of. Toxic biomes are also a option maybe with a dead transistion zone surrounding it. A toxic zone could come in different varieties and be home to strange nether creatures and mutants. If we want to make toxic zones places that a player might want to explore than you could have certain chemicals be harvesteble or refinable from the various flora and fauna that live there.
I don´t think that combining there two approaches at the same time though is a good idea. This would simply up the difficulty to the point that it would be better to make it into a mod.
What I like most of this idea is the concept of beneficial plants and the potentials for renewable resources. Like a steady source of renewable metals or poisonous hedges you could surround your home.
It might be crazy to even say this, but maybe even a mutated supersized pumpkin the size of a house could be helpful in establishing a quick base setup. Though maybe I’m stepping over some boundaries here.