Safe Lithium Battery Management
Batteries are tricky nonlinear devices. If you want to build a safe and reliable lithium battery charger, you need to know more about your batteries and your battery charger circuit. In general, lithium batteries are not interchangeable and not all chargers will work with all batteries.

There are also significant differences between lithium (probably not what you mean), lithium ion (probably what you mean, sometimes written Li+ or Li-ion), and lithium polymer (sometimes written LiPo) batteries, and significant differences within the battery chemistries of these categories.

The datasheet I found for TP4056 does not say that this device includes undervoltage protection. It only provides charging. Perhaps other circuitry does on that evaluation board does. The appropriate discharge protection is a function of battery chemistry, and the threshold should set according to the battery manufacturer's datasheet (as a baseline, anyway).

A circuit that tests for undervoltage is probably measuring the battery under load, and will need to compensate for the battery's internal resistance \$R_{internal}\$ reducing the voltage at the terminals \$V_t\$. That is

$$ V_t = V_{oc} - IR_{internal} $$

So to answer your second question it's quite possible that \$V_t\$ = 2.5V is an appropriate cutoff for a battery with \$V_{oc(min)}\$ = 3.0V, if \$ IR_{internal} \$ ~ 0.5V.