In Vajrayana, everything is about practice, and there is no point in trying to build a grand theory of everything.
In Vajrayana, there is the "trinity of refuge practice", a bit different from the Sutric refuge, and there is also the "trinity of the Buddhas" that is expressed as the Guru, Ishtadevata, Daka/Dakini/Dharmapala, or Lama, Yidam, Pawo/Khandro... or Teacher, Deity, Dakini/Protector. These triune objects act as either the objects of the Tantric Tri-fold refuge, and also as "the three faces of the Buddha". As tor the refuge, the Teacher acts as the Buddha-jewel, the Yidam as the Dharmapractice-jewel, and the Dakinis and Dharmaprotectors as the Sangha-jewel. As for the identity of the Tantric Three Jewels, the Guru, Yidam and Protector can be taken as a single principle of Dharma-source, manifesting in three different aspects of the source, the Buddha-jewel - or even as in sometimes: the Guru is Buddha, Dharma and Sangha.
So, in one sense, the Guru, Deity and Protector are the same, the Buddha-jewel. And yet, they are not, as it is clear that for instance the Guru might live in England, the Yidam being me the practitioner, and the Protector being someone I ask a favour while residing in non-england. The identities and so forth of all these things do all depend on what you practice at a given point of time. No grand theory is asked or available, only separate practices.
The practice of Yidam is about being the Yidam, and that is something one does not do with Protectors - the Dharma and Sangha being different. So no, Shugden is not to be counted as a Yidam. (You might be Guru-Manjushri due to guru-yoga and completion stage practice, and the Guru and Protector might be Manjushri due to some emanational occurence, but nevertheless, you would not be the Protector. Yidam and Dharmapala are not same, no matter how much they both are Manjushri.)
The idea of Fourfold refuge, where the Buddha, Dharma and Sangha are united in the Guru, adds of course more confusion to the situation. But nevertheless, Protectors are not Yidams, as the practice is different. It would be good, if people would practice, not speculate. All the different mandala-classes present different worldviews, and to even to try to get or formulate "a grand unified tantric theory", is doomed on the outset. In Vajrayana, there is only the practice which is rather clear and easy, but the theories, even the canonic theories do note, are in contradiction among themselves, and only muddy the waters of Dharma.
Dorje Shugden is a Protector, who helps the practitioner in his or her ethical activities, be they daily, Sutric or Tantric. The practitioner is nevertheless not Dorje Shugden, and the practitioner cannot practice in a manner thinking he or she would be.