1. <pre> tags will ignore all wiki and HTML formatting so if you use them you would not be able to provide links to other profiles (individuals or freespace), or external webpages, <ref> tags for sources would not work, templates would not work. Never mind actual formatting of the text (colours, size, headings, tables).
2. Wikitree like every other wiki in existence is really meant to be used online.. "born digital so to speak"; import and export of gedcom is somewhat of an added feature but is not really the purpose.
If you open the gedcom as a textfile in your word processor you should be able to make all the changes for an entire Gedcom fairly quickly using find and replace find and replace... especially if your software supports regular expressions.