I have never spoken to an Appraiser about it, but, yes, Clients seem to "dis" the flat-tops:
There no snow in San Mateo; it just seems to be their opinion.
I can just imagine that an Appraiser would gravitate toward other Eichlers for Comp's,
which means that it might be a little hard to do Comp's on one.
If you don't care, and you plan on living there a long time; I would suggest not worrying about the discount on an Eichler. Do what feels good to you.