We have also had this issue. We are a very small, family-run operation, in a very rural town in NE Washington.... We don't deliver EXCEPT for large orders to the Gold Mine that is nearly a 90 min drive (we are the ONLY Pizza restaurant in our entire county (in 1 hr drive in any direction) Because its our largest repeat customer, those bottoms getting soggy is a concern. Although we do put the boxes in the warming bags for transport.
We've looked into a several of options, some we got from the PMQ ThinkTank of box liners that allow the juices from the veggie pizzas drain away so the cut crust doesn't soak it up. I've seen corrugated liners (Like a half sheet of cardboard ripple stuff, there are some high end white dimpled paper liners that are very expensive unless you can order in a quantity to get the per unit price way down. We have never tried the corrugated ones, and the white paper ones still got soggy in our test trial.
We also found some cut plastic screens (looks mesh like the screens we build our pizzas on and bake in our brick oven) and out of all that we've tried, we found the plastic mesh the very best option.....only again very expensive for our very low volume. We do have some customers who must drive home 40 min - 1 hr away who just won't buy our cooked pizzas because of the soggy factor by the time they get home. We have tested this white mesh plastic liners with these customers, and ask that they are careful with them and bring them back. They've been very happy as the crust does not get soggy! They are easy to clean and sanitize in our dish washer. We have not yet ordered a supply trying to justify the cost to put these into our production...but if we do, we will likely charge a small deposit fee to be returned when the customer brings the liner back... its the only way we can think to justify what goes out our door. Next, at least for customers who drive such a long distance and who do not want a 'take-n-bake' pizza, we've also suggested they ask for their pizza to not get cut at all when they order. By not cutting the crust until just before they eat it, is a tip I got from a lifehacker site a couple of years ago.... I know not cutting the pizza for large orders is not practical however.