Interesting. If the time to build modifier is based on size, rather than cost, then I expect merchant ships to get quite big.
That way, you tie up fewer slips for a given volume of shipping.
But as tech gets bigger, ships get more expensive per ton, so warships won't get as big as fast.
The only thing increasing merchant ship cost per ton will be increased engine costs, but some earlier analysis I did suggests that as engine cost increases, the proportion of space on a merchant ship devoted to them will decrease. So while early merchant ships may actually be faster than warships, as tech increases, efficient merchant ships will be slower, and only specialized merchant designs will be able to keep up with the fleet.
The size increase also makes a big argument for Jump Gate construction.
Consider:
A race wants to be able to shift truly large amounts of infrastructure and industry. It can go with a design that takes 1 year to build, or one with 8-10 times the capacity in 4 years. It would have to build really large maintenance facilities, but when considering the possibility of terraforming worlds with multi-megaton duranium deposits, large ships look to be a bit more efficient.
A downside is that by building very large slips a race can go through a stockpile VERY fast. And a bad guess about what size is efficient would be very costly indeed.
And here is another plus:
If you are interested in avoiding the Total Warfare paradigm of Starfire, this makes it possible to build very large planetary monitors that CAN'T go on the offense, due to a lack of jump ships. So wars become a matter of lesser ships duking it out on the frontiers, for limited stakes.