Assuming you have a common 130/74 mm bcd road crank, 38T is the smallest you can use on the outer bolt circle so the 39T is not worth changing. You could install the 39T ring on the outside of the spider if you wish. In any event, a single chainring will require a set of shorter chainring bolts and these are available.

Using the inner (granny ring) position only will indeed give chainline problems.