Yeild on the geothermal site has been increasing since the start of my current game (ver 0.16, started just before 0.17 dropped). The site started at 100% and is now close to 3000%. Please advise.

hurry up, start the rocket and flee from the planet before the geothermal site or even the whole planet explodes :-)

And it is true))
Thus, the resource is increased only at the starting area, after studying the technology "geothermal source", and then with each new technology studied.
I thought it was necessary or not, but in the end I did not refuse. You still can not put more than one geothermal reactor on this spot. Any other resources found on the map are not replenished.
You can open the control.lua file yourself and comment out the following.

script.on_event(defines.events.on_research_finished, function(event)
for , force in pairs(game.forces) do
for ,research in pairs({"termal"}) do
reapply_research(force, research)
end
end
end)

To do this, put -- before each line, It should look like this

-- script.on_event(defines.events.on_research_finished, function(event)
-- for , force in pairs(game.forces) do
-- for ,research in pairs({"termal"}) do
-- reapply_research(force, research)
-- end
-- end
-- end)
And your resource on the starting area will not be replenished.

There is a better offer, just uncheck the settings
Version: 0.1.0
Date: 27. 02. 2019.
Changes:
- In the game settings, you can enable and disable the replenishment of the geothermal source at the start zone, after learning technologies. Enabled by default.

Ok so it was supposed to happen. Does the geothermal site dissapear after it zero's out?

I did not check it, the geothermal source was copied from oil, so if the oil disappears, then it too.
...walk and build does not interfere

Then no. There are mods that deplete sources completely. I do suggest looking into them to see how to remove and include as an option.