1. So what if your timer needs 4 digit with multiplexing you can drive any number of digits whats the problem. Looks like you are worried about number of pins needed. You will need 7 uC pins connected to the 7 segments of all the FND moduels and 1 pin each to select a particular module digit. i.e You will need 7 + 4 = 11 microcontroller pins to do this task.
2. Driving the 7 segments directly will increase your program length maximum a page but your hardware and cost of circuit components will get reduced.

Regards,
Prahlad Purohit