It is one transaction, thus one set of docs, that should encompass all of the costs associated with the one transaction, as complex as it may be.
If both properties will secure the loan, then just think it through: double the flood cert estimate, double the appraisal estimate, double the title work, etc... It will all work the same way, just with bigger numbers, because there will be more costs associated with obtaining the loan.
As Truff often points out, the GFE and HUD are all about the costs to obtaining the loan, not the home(s).
I don't repeat gossip, so listen closely...