If you look at the BCW pics in John's first reply, notice that the boxes that have multiple chambers have a deep cover. You can take advantage of that for the slightly taller cars/engines...the ones with horns, whistles, etc...by adding a sheet of the foam to the inside of the cover. The deep cover will stay put on the main box, but the foam cover liner will give you that extra top protection. The single BCW boxes, as shown, by their nature don't give you that cover advantage. I tend to not use the singles for those fragile-top situations you mentioned.
BCW offers some interesting discounts from time to time. The boxes cost less if purchased in quantity...something those of you in clubs might want to consider. Our LHS has a sizeable games department which likes to offer the BCW boxes for their customers from time to time. You might be able to join in one of their purchase orders if you have a gamers retailer/LHS nearby, and gain some cost advantage in the process.
And, the other BIG advantage of buying in quantity is survivability of the boxes in shipping from BCW or their dealers, wholesalers. Boxes are shipped FLAT...meaning you will need to fold them up into their final shape...an easy job. NO ONE ships them to you pre-formed. Ergo, if you have a discounted bundle of box flats shipped, they will have far more survivability through the shipping process than if you order fewer.
FWIW...
Another Ken