Terminals have a fixed character width and height, and most (all?) terminal application programs make the window an even multiple of that size (then add the window title, some margin around the sides, etc.), so there will never be a partial row or column visible.
They could theoretically add more margin at the right/bottom of the window when the window is zoomed out, but then your question might merely be replaced with someone else asking “Why is there always some blank space at the window edge when the window is zoomed?”.
And what should happen to the window if you resize or show/hide the Dock (for example) such that the window is no longer the same dimensions as it would be if you zoomed it again to fit the new display area? When you Zoom a window, it isn’t placed into a “zoomed” state, it’s just resized to the current available display area at the time you Zoom it. If the available display area changes and you haven’t asked it to Zoom again, then what?
Not that these aren’t solvable, but there are a number of dynamic behaviors to consider, and terminal applications typically keep things simple.
Note that Mac OS X Lion “Full Screen” is an actual state that the window is in and Terminal always fits the window to the size of the display, updating when the display size changes, and adds margins as mentioned above. The size of the Dock, for example, is ignored.
Best Answer
You could try to achieve this functionality with an application like "Afloat" as you mentioned already. But it seems to only work in El Capitan if you permanently turn off System Integrity Protection (SIP) which isn't recommended.
However, here is the link to the program: https://github.com/millenomi/afloat
How to turn off SIP: https://github.com/millenomi/afloat/issues/22