This is interesting since I have (currently very poorly) engineered boosters which give +45% (average) resistances across the board. Does this mean that essentially all I need do is focus on the boosters (engineering-wise)? Not to say that some heavy-duty engineering on the shields themselves wouldn't go amiss...
Well for your purposes of PvE combat we're talking about the two most conventional Shield Generator mods: Thermal x Reinforced.
Thermal will plug the obvious resistance hole immediately whilst providing some boost to the total amount of shields, thus making the resistance profile more even. Apply some Resistance Augmented Shield Boosters there, then (each can go up to 12,5% resistance boost across the board, not counting God rolls, not counting diminishing returns). After the third or fourth Resistance Augmented SB, make the rest Heavy Duty (for the boost to the total amount of shields, and because of diminishing returns). Since the total amount of shields won't be the best, it will recharge % faster.
Reinforced will give a huge boost to your Shield total amount, but will carry the same poor unbalanced resist profile and trying to patch it with different specific Resistance Shield Boosters (Thermal SBs) the nerf to the other resistances can make the final resist profile turn out to be poor when compared to the above. Since Prismatics regen really slow, might as well just go with total amount for big ships since the regen benefits given by the Thermal Gen tactics won't be so expressive (in comparison) in real combat anyway (say a CZ, for example).
Some people go full Reinforced with Resistance Augmented SBs plus some Heavy Duty SBs on Prismatics and just low wake when low on shields, Reboot/Repair to immediately regain 50% shields and they're good to go.
To each their own.
Answering your question, engineering the SBs is as much, if not more, important than the Shield Gen. SBs are OP.
What is the reasoning behind the smaller boosters?
Less power hungry. I've just forgotten to not roll so high on the PP, should have gone G1. Also, Heavy Duty on smaller SBs is more bang for your buck %