Just stumbled on this discussion by chance... I was given the crystals when I received the life entrustment from my lamas. I was told that Dorje Shugden resides in that crystal; however, it was also made clear that Dorje Shugden will be present anywhere where the Buddhadharma is present, especially the teachings of Jamgon Tsongkhapa (all my lamas have said that wherever there is a text of the Lamrim Chenmo, Dorje Shugden will be present with it).
ChoDorje, my lama has said the same about Dorje Shugden being present wherever the BuddhaDharma is. I have heard a little of the significance associated with the crystals being received during sogtae, some to do with the bond it signifies between protector and practitioner. I am a great believer that such items, along with chakras and pendants have power, protection and great blessings, particularly when it is blessed by a holy lama such as my teacher, prior to receiving it.
Likewise, as long as we hold the BuddhaDharma in our hearts, and do what pleases Dorje Shugden most, hold our vows, practice guru devotion, study the lamrim, he will always be with us and watch over us. We don't need a pendant or chakra to receive his protection.