First of all...what type of background did you apply your mortor too
Second...how thick did you apply it.
Third...what type of Mortor did you use.
Fourth...how many people do you think make mortar walls LOL...
If I were to do this type of work, I would first attach some type of metal or plastic lathe over the wood I wanted to apply the mortar too. Secondly, although not necessary, I may built up my mortar to at least 1/2" thick...likely two coats of 1/4" each. With my first coat, I would use two types of sand in my concrete mix...a coarse aggregate, and a fine aggregate. Let this set up over night.
Next, I would apply a fine coat...two types of sand...fine sand, and very fine sand mixed with the portland cement. This will give you a strength undercoat with a nice smoothe (although texturable) finish coat.
For sealing it, you can use most concrete type sealing products...like Thompsons for concrete. I don't believe it will take away at all from the naturalness.
John Eddington