Maybe it is positionned under the ground?
Ok, I need glasses apparently.
What I figured out
First I tried your suggestion, It just raised the question point of the save mark up in the air. So I reset what I did by copying flevel out of the steam default file. Went back and saw that the flame on the savepoint was very faint anyways. So I moved it again and I saw this time that it was there. Checked the original pic and noticed slight discoloration that looks like its there as well. Default steam game even has the flames as very faint for some reason so it wasn't 7th heaven or any mods that were causing the flames to be faint. I'll probably work with a different save location from now on. Just so I can see everything up close when I try experimenting on other things. Probably the Midgar tutorial room. Thank you for the suggestion but it was me being blind lol.
Edit:

Did experiments and moved savepoint. Save Point turned into Hard Hat man cause I had deleted all other model groups aside from cloud/party and one listed save. Tried adding Yuffie to the end of the list of NPCs and added her model to the map. But ended up in an odd position. When I talk to the materia it says what I copy pasted for it. Yuffies model obviously shifted what models show up where since I on accident spawned her in the middle of the list. I had to reset flevel when I tried to delete her model and put Nanaki in it's place. Which is where I'm at right now. Hoping that making sure to add a new model at the end of the model list will give better results.

Whew! That was the problem with the model. Added small script to give all Materia and it worked. I didn't set any stop to it though so anytime you walk up to her you get another (whoops). But feeling good that I can mess with on screen NPCs. Not sure what to do next, probably go somewhere to see if I can mess with walk mesh. Maybe add a climbable vine to the cave in the ancient city and see about adding a new area.
Edit: and some hours later I'm fiddling with placing a ladder on the coral valley vine going up to the walkmesh in front of the cave. I feel like I almost have it but coordinates are off slightly. Plus at this point I have distractions at work (half my shift is easy with no one bugging me but the other half...) and I've been trying to figure this out for hours with my only breaks going towards my job. So I'll see if I can get it to work tomorrow.
Edit: Apparently ladders are complicated lol. I'll go look at some other ideas and come back to it.
Edit"
https://youtu.be/3gL7jyiUy5EMWAHAHA! HA!HAHAHA!HAAAA! Ok it was a donkey and a half but I finally got the vine to work. It was seriously just rolling numbers and copy pasting ladder from bone village until I got it to work.