Is it possible to just pay a shipping container company up front to use materials that are more friendly for repurposing, with an agreement that you buy it after it is used? That way you wouldn’t necessarily need to strip and repaint it.
If one wants to avoid stripping paint and floors out of secondary market boxes, it's also possible to buy the constituent pieces of a shipping container individually - the corrugated sidewalls, doors + fittings, floor channels, corner castings etc - unfinished or with primer only. In this way, you can ship one or more deconstructed shipping containers INSIDE a shipping container! But then you have to fixture it and weld it etc, so you're back to losing economy of scale...
For our purposes, we usually use 1-trip/low-trip for client projects avoiding the nasty ones by careful selection, and we have a custom machine that media blasts the interior and exterior down to bare metal when we work with older WWT and partial/damaged containers of unknown heritage.