compact project, powerering and charging

BruceM:
the batteries I have looked at do have discharge protection built in.

Make sure that the low voltage cut off is 3.0V or more, you will need to check the datasheet for the battery.

A lot of these 'discharge protection built in' things cut off as low as 2.4V.

From Wikipedia;

Voltage cut-off in portable electronics

Some portable equipment does not fully use the low-end voltage spectrum of a battery. The power to the equipment cuts off before a relatively large portion of the battery life has been used.

A high cut-off voltage is more widespread than perhaps assumed. For example, a certain brand of mobile phone that is powered with a single-cell Lithium-ion battery cuts off at 3.3V. The Li‑ion can be discharged to 3V and lower; however, with a discharge to 3.3V (at room temperature), about 92–98% of the capacity is used.[2] Importantly, particularly in the case of lithium ion batteries which are used in the vast majority of portable electronics today, a voltage cut-off below 3.2V can lead to chemical instability in the cell, with the result being a reduced battery lifetime. For this reason, electronics manufacturers tend to use higher cut-off voltages, removing the need for consumers to buy battery replacements before other failure mechanisms in a device take effect.