For the Site Parameters, when would one want to (or not want to) specify the "MTL-NAVD88" correction used in the Elevation datum conversion? What is the purpose of this parameter?
Nearly all elevation data are specified in terms of a geodetic datum (http://en.wikipedia.org/wiki/Datum_(geodesy)) as opposed to a tidal basis. Tide ranges are poor bases for measuring elevations as they are temporally variable on both a short-term and long-term scale. Fresh water flows can also affect mean tide level and other spatial considerations within estuaries and shorelines.
However, SLAMM needs data expressed in terms of tide ranges as marshes respond to tides not fixed vertical datums.
Therefore, you must convert the data to an "MTL" vertical datum basis.
You can usually use data available from NOAA gages or the NOAA VDATUM (http://vdatum.noaa.gov/) product to produce this conversion. You can also input a spatial raster as derived using VDATUM.
Also see this thread (http://warrenpinnacle.com/SLAMMFORUM/index.php?topic=79.0) please.