the bass reflex port, depth and diameter and location makes a diffirence. adjusting diffirent sizes to match the woofer to reach desired sound is tuning.
wide with smaller bass port cylinder gives louder bass.
increasing the bass reflex port cylinder to midway will reduce high bass and clear low end bass,
increasing the cylinder length further will keep on reducing air vent and lowering the bass
depth of box usually increases the low end frequencies, but in car there is limited space.
placement of woofer closer to ear level instead of foot area will increase its sound for yr ears sitting in driver seat. so trunk is better option
as you have noticed the 6 by 9 speakers on rear dash give quite refined bass, being on a certain angle to ears.
further more crossovers help getting the desired bass.
if you overlap woofer bass with rear speakers bass, it tends to get more muddy. (high end bass notes get amplified.