Do you see that diagram says "gap approx 40 cm"? Do you see that I already told you they deliberately designed their submarine to be 31 cm in diameter? Do you see that there's a chance that the oxygen tanks and their human chest combined are indeed more than 31 cm, and hence having to take them off might not say anything about whether a 31 cm tube will fit?
I can see that but I can also see that there's an air tank mounted on the outside of the submarine. This could probably be taken off while passing the narrow passage.
On the other hand you would need to squeeze a person in that submarine over the whole diving range. That would probably not help feeling them more comfortable.
Last not least in article you will find the quote "'The equipment he gave us is not practical for our mission,' Narongsak said Tuesday morning", that might prove my point.
Finally I don't get why you are arguing that the submarine is such a great idea when it's clearly not.