Female pin-header on top of the board
For school use it would be better to use a female socket to prevent pins getting bent or shorted. At first sight ribbon-cable plugs with pins are difficult to find and expensive, but a male-male gender-bender is very cheap and easy to find. A female-female gender-bender is a length of ribbon cable.
If an accessory expects a connector on the bottom and it is on the top (or vice-versa), then a length of ribbon cable can be used, with gender-benders as required.
Consider the situation where an accessory is expecting to be plugged directly into the RPi, but the wrong gender connector is installed. If both are female, then a male-male gender-changer can be used. But if they are both male, you would need a ribbon-cable, and the boards would not be tied together.
A male shrouded header is keyed so cables cannot be connected backwards. In fact it is easy to find a cable with no, or incorrect, keying. There are N/C pins on the GPIO connector. They should be blocked on the female socket and the pins removed on the male plugs. That then provides fool-proof keying.
Standardise on a Female pin header on top of the board with N/C connections blocked. Any variation can be accommodated with a suitable collection of adaptors.
Avoid connectors on the bottom of the board as they would foul many case designs.