There are many simple reasons why this could be the case.
1. 32gig chips may be older chips. We had 32gig capacity iPhones for a while chances starting at the 3GS they may be still using the same chips from 7 years ago. Why use those old chips? Probably because they are cheaper then brand new 32gig chips. And people buying the 32gig model get so because they are cheaper.
2. Fragmentation iOS and your apps take up a lot of space. Small storage increases the chance of running into fragmented storage needs so duping that 4 gig will need to broken up a bunch of times to fit. While the bigger devices have free spaces in huge chunks.
3. Less then ideal driver. Being that most people will not be using their 32gig phone to store a lot of data. The driver/os may not be optimized for write speed or if using an older chip there may be extra error checking or error checking added to the 32gig chip driver.
Conspiracy everywhere logic is quite tiring. The closest to a conspiracy I have seen is mostly laziness in the organization who will stop and say that it is good enough to be released.