Go for it,  I love that players and their characters want to throw in and make their ship better as its their money maker.   :)     So buying the materials and having the siege engineer build it is fine.   He can roll it and my id for dice roller is 714 and of course  because this being done out of dangerous situation and with time the roll can be at a take 10.   However the check is at 25 so one might want to take 20 on the DC.   however that means that there was some failure or flaws that were corrected as the siege machine is being built.  So if take 20 is used a penalty of +25% for cost of materials will be accessed.    O:)