If you want a stock daily driver engine, the '86 is fine. Plus, it produces less emissions, especially at idle. However, if you want to add heads, then you don't want an '86 shorty block. The '86 setup has better
low-end and mid-range power and torque. So, for a daily driver, it's great.
For the quarter mile, you get very limited in heads and cams because of the flat top pistons. In fact, the only other head that
meets spec for valve to piston clearance is a TW head.
As mentioned, the upper and TB are different (targeted for low-end and mid-range response and power). The heads are E6 high swirl heads (better idle quality and lower idle emissions). The pistons are flat tops (less likely to cause pre-detonation, but limit the head/cam choices).
It's called
real-life trade-offs in any engine design or setup.