The formula Availability=Uptime/(Uptime+Downtime) is the most general, and therfore will ALWAYS be correct.
The expression MTBF/(MTBF+MTTR) holds only if ALL MTBF & MTTR assumptions are in effect, and these assumptions are another, extensive discussion which is beyond our scope.
From the prctical point of view, Uptime is the interval during which a system is available WHEN WE NEED IT, and Downtime is the complementary period of time.
Downtime can result from faulty system, maintenance (both preventive and corrective), inspection/calibration, and sometimes also power-up and set-up etc.
A major contributor to Downtime is logistic times, during which a system is unavailable due to a missing part, an unavailable technician etc.
The formula for the availability you gave is true if and only if the failure probability density function as well as the repair / restoration pdf are exponential, and only for steady state (t goes to infinity). Like it or not, this is the mathematics behind it. Find a detailed explanation in Monte Carlo Applications in Systems Engineering, by A. Dubi to figure out more. The easiest way is to ignore it, but then any preventive maintenance consideration is a mathematical violation.