Just place a "thick" LP under the new mat (really thick would be around 2mm/really thin would be around 1mm) and see if it sounds better after readjusting the VTF.
The VTA of the stylus comes first, IMO.
I've owned many, many, many decks with SME arms, without the arm being totally parallel to the disc/platter, and they all sounded super once I dialed in the VTA.
I assume that "parallel" may be a bigger factor on some arms, but I have not experienced such with my older (various) SME's.
DeKay