Well your setup looks exactly like mine did when I first received it (from Sweetwater). I would have sent it back but after playing it for a short while
I decided I didn't like the neck at all anyway. The nut end is too narrow (my opinion... and I have skinny fingers) and was cut way too deep at the factory.
The strings should not be completely below the top of the nut like that (especially the larger flatwound strings). The excess height at the bridge end
was due to the trem posts being too high. Dropping them (just thread them in deeper) would have helped that end but with the crap nut, the buzzing
would have been unplayable. I have since replaced the neck with an all maple Warmoth 16/10 compound radius with a 1.75 tusque nut.
One thing I don't hear mentioned when swapping the necks on a 69 is that the hole pattern is 'not' identical to a Strat. One of the attachment holes
on the 69 is offset and requires a new hole be drilled in the body (no big deal but should be mentioned). If you're otherwise happy with the dimensions
and feel of the neck, I would still recommend replacing that nut. There are a couple of ways of fixing it but I would not recommend shimming up the
entire nut from underneath because of the excessive depth of the slots. Checkout Youtube for some other ways to 'fill' each slot and re-adjust the depth.
It won't be all that it can be with 'that' nut.
Have fun !
https://www.youtube.com/results?search_query=guitar+nut+repair