Sorry cant give you the scientific references you ask for (too lazy to search for them) but Ill give my 2c worth anyway (just regurgitating what I have read which may or may not be scientific - like most body building knowledge).
If your muscles experience an increase in the cross sectional area of their contractile elements then they will get stronger and they will of course get bigger too.
Your muscles can also experience an increase in their energy storing/producing units (by increasing number of mitochondria or something), that will make them bigger but not stronger (but able to last longer before tiring).
Your muscles can also experience an increase in their neuromuscular efficiency. That will make them stronger but not any bigger. (Your muscles have some fancy sounding nervous reflex which limits the maximum load you can lift to below the max they are capable of. Training can increase this self imposed limit of the nervous system.
For one thing at any one time only about a maximum of one third of your muscle fibers are contracting - as muscle fibers tire others take over. Presumably if you could get them all contracting at once you could experience quit a strength increase albeit probably at greatly reduced duration. So there is quit a bit of potential for increasing strength through increasing nervous system efficiency - which obviously doesnt increase size).
I too think that this functional and nonfunctional strength business is largely BS. Unless as the poster above says youre talking about building up to a Ronnie Coleman like 140kg then wanting to set records in long distance marathon running for example.
This business about you train your pecs to be strong at one type of exercises then get them to do a different exercise that involves pecs and suddenly theyre all weak at it because they havent seen that movement before is BS in my opinion (and personal experience).