We also started with the Godot Wild Jams and trying to make our games accessible with multiple input methods. It can certainly limit design choices and make you really think on how best to handle input.
It is good practice to make sure all instructions are in game. For a jam putting them on the game page due to time constraints is reasonable, but as you continue to develop I'd try to put them all in game. I do not see any mention of pressing Esc/C/R1 to cancel building in game. In that vein, I'd add a setting to change which controls are shown on screen, between keyboard and joypad.
For the current 3 towers, your joypad controls work, but if you add more, you'd eventually run out of buttons. You may want to have 1 button to start build mode, with the last selected tower, and use L1/R1 to move through them. This is not as fast as a dedicated button, and requires a bit more paying attention to which is selected, but would allow for additional towers. One option for speed, would be to have the top button (triangle) start with the last selected, while the left (and right buttons (square/circle) start at preset towers, spread out among the options. This would allow quick access to placing multiple of the same tower, but also allow starting at known positions. If you had 9 towers, and started at #3, you could then know to press L1 twice to get to #1. Still not as fast as keyboard with being able to press the number and get there in 1 press, but allows a bit more speed within the constraints of a joypad.
With keyboard, the tower placement puts the tower in front of you, while the controller seems to favor having it on the same tile as you. It would be nice if the 2 inputs were consistent in the positioning.
When you are in tower placement mode and the tower details pop up, the tower list moves down. I'd recommend adjusting it so the tower list is anchored in the lower position.
There should be some sort of timer or push for the player to advance. While writing these comments I left the game running in a background tab and built up a lot of corpses. Obviously, this can be something for play balancing later, but it was something I acknowledged and used as a strategy. I restarted and built 3 Dead Towers, then waited while a bunch of enemy troops came in and were defeated. Then I'd advance until my Dead Towers could hit the enemy towers and place 2-3 of them. Once the enemy Tower was defeated, I'd build up more corpses before taking out the town buildings. Then I'd advance and do similar for each town. I'd build enough Dead Towers to cover me, while staying our of range of enemy towers to place a line of Totems. Then I'd start my wall of Dead Towers, while watching my health and after every 2-3 towers placed I'd move back to be healed. The tower placement was a quick move out then down placing the towers on consecutive tiles, trying to avoid getting hit. With the Totems already out, this went quickly.
It would also be nice if the game over screen included some stats, such as how many towers and skeletons built, how many enemies defeated, and how much decay had been spread. I went back and covered all the tiles I could before advancing to destroy the last structures. I placed a tower too close to the final flag building and destroyed it before I could cover all the tiles.
Personally, I'm not a big fan of the death/decay theme (I know it was last month's GWJ theme), but the game itself has a good foundation and was fun to play.