I'm sure the OP is long beyond needing this information...but as it was necro'd and some other questions came up I'd like to help out a bit.
The Laboratory Ship mustering out benefit is literally the ship called the Laboratory Ship on pages 121-122. There's no need to convert another ship into a lab ship. The five ship shares you receive when you gain the "lab ship" benefit is for this ship only. If the player wants a different ship, he only gets two ship shares as noted on page 35 of the core book. This rule holds true for all the other named ships you can gain from mustering out. Free traders, corsairs, et. al. are the ships listed in the book as such. You get 5 shares if you pick that ship, 2 if you want a different ship. Of course you can deviate from that all you want, just wanted to share how the rules were intended.
Now, if you muster out with a the lab ship on pages 121-122, there's nothing to prevent you from gutting out all the lab space for cargo to use it as a cargo ship. As it's 100 tons of space dedicated to those rooms, you'd free up a significant amount of room. Heck, the lab space isn't even listed with a cost, so you can safely assume the labs are empty rooms on purchase, and all the areas on the map designated as 5. Labs could easily be used to hold cargo.
To the few that were confused by the maps provided on 122, look at the picture on 121. The left hand two maps don't stack, they wrap around in a circle. To visualize, imagine taking the two sections of map to the left of page 122 and taping them together to form a loop. Where you see the letters A & B at the top and bottom by an iris door, that's where the maps would connect. All of the other areas stack on the 1. Bridge/Avionics area. Below the helm area is the sensors area, and above it going upward are the quarter deck, the engineering deck, the two fuel decks, and then finally the flight deck which would be at the center of the loop.
The pictured ship on page 121 isn't truly representative of the maps and stats, but it's close enough to understand how the ship is laid out. The skinny tube running from the outer ring to the inner area in the picture should be a lot thicker, and the center cylinder shouldn't be so large. It looks like that picture was drawn to look like the MegaTraveller era Lab Ship, which isn't an exact match the Mongoose generated one...but it's close enough to help understand how the ship is meant to be laid out.