My interpretation is that one would eject from the whole engineering section in the original setup, with the bottom of the long core already touching the bottom hatch of the chute.
That the modernized system would place the miniature core at the top is just one oddity in the setup. The other is having a single core when there are two engine rooms, supposedly both with an end hatch pointing towards a core. But here the S1 VFX and the exterior detail are in agreement about the obvious idea: that the engine rooms are at an angle wrt centerline, following the angled surface contours, and converge at one and the same warp core...
...Which really would be farther towards the bow than shown in the S3 ejection. But perhaps they took the old chute and moved it? After all, they appear to have taken plenty of old corridors and moved them to new locations on the edges of the extended neck and recontoured rings. Possibly the whole ship briefly became malleable goo in the throes of programmable matter clouds, and emerged slightly rearranged, with just 5-10% all-new bits?
Timo Saloniemi