Dimensions and Biomes: I have some questions

- The first quite embarrassing thing is that the player spawns above the void. Make it endlessly fall into death. Does anyone has a fix for that ?

You could make a structure that spawns when the entity enters the dimension. Have it hooked up to a global variable that is false by default, and when it's generated turn it to true so that no further structures will be generated 

- My second question is: Can we have a custom colored sky? I changed the air color of my biome but in the dimension, the air is totally normal and the sky is blue

I'm pretty sure in the biome AND dimension maker there is an option to have a custom sky colour, so change it in both.

- My third question is: Can we have only one type of flower/plant that spawns in the biome ? We can put vanilla flowers but it's spawns all kinds of flowers. I thought about making a structure with only that one flower and make it spawn everywere in the biome, but I was hoping there was a more simple way to do it; if so, please tell me.

This isn't in mcreator yet, but there is a ticket for this, so you can vote it to get it added faster! 

A dungeon spawned in. I don't want vanilla dungeons to spawn in my dimension. How do I prevent this from happening?

Unfortunately this is not possible. (yet, i hope)

Also, I've made trees in my dimension, but the leaves that I've made ( they are block base: leaves) disappears as if there is no logs. How do I make a log-type block that keep the leaves alive and prevent them from disappearing ?

If you have a custom log that you want to act as one (keeping the leaves alive), I would add that block to a tag to make minecraft reconise that as a log. Add your log to the "logs" tag registry name, make it a minecraft tag and set it to blocks

I would recommend checking out the mcreator youtube playlist for more information on tags and such: https://www.youtube.com/playlist?list=PLAeL-oIFIEngE6jRgFYeFMfuj8WQsO3Ei