Using "track nails" has its own issues, namely (over time) the nails tend to "lift" and will then catch on the trucks/axles of your engines and rolling stock. No need to go into the issue that will cause I don't think. The other issue with them is what they are being "nailed into". They will go into homosote and foam easily BUT the afore mentioned issue will occur quicker and more often. Trying to hammer them into ply is a "hit and miss" experience. Some will go in okay BUT others will bend and not go in flush causing potential problems. Track Nails are not all that strong, so bending them is not a difficult thing to do no matter what you use to "try to put them in". Once again, the issues with track nails is from experience.
If I were you, I'd go with the water based or acrylic caulk - quick, easy, strong and reliable.