The application of hate crime legislation is based on the motivations of the perpetrator (and thus not on whether a victim actually shares one or more of the characteristics protected by the Bill).
The latest Crown Office and Procurator Fiscal Service statistics show that, in 2019-20, 41 charges were reported with an aggravation of prejudice relating to ‘transgender identity’ as defined under the Offences (Aggravation by Prejudice) (Scotland) Act 2009. The definition in the 2009 Act is wide enough to encompass 'non-binary persons', 'persons who cross-dress' and persons with 'variations in sex characteristics' (although those are not the terms used in that Act).
In terms of specific evidence in relation to 'variations in sex characteristics', although it is noted that more research is required, the Equality Network believe that people with variations in sex characteristics, or people perceived to have variations in sex characteristics, can face hate crime. In one of its hate crime research reports , they found that 29% of respondents with variations in sex characteristics had experienced hate crime based on having variations in sex characteristics (although noting the small number of respondents).