The new IcoMoon app itself takes care of evenodd fills, outlining of strokes, and uniting all paths. No need to modify your SVGs before importing for font conversion.
Interestingly "svgo", the popular SVG minifier, doesn't seem to support converting "evenodd" fill rules to "nonzero" fill rules, which is something that you need both to support "evenodd" SVGs in icon fonts and to merge multiple paths together in a "evenodd" SVG.