Armour Synthesis turned out to be a disappointment for many Destiny 2 players, especially those whose obtained pieces are not available for transmog. Bungie clarified why this is the case.
Bungie released the first TWAB in Season of the Splicer, revealing why some of the armour pieces are not appearing for transmog. They previously noted that the Solstice glows would be unavailable but there is also the matter of the Gambit Prime armours whose looks can't be reacquired.
The TWAB in question stated that there can be two reasons why obtained pieces are not appearing on the cosmetics screen. First, the transmog option won't appear in the menu if you are already wearing that part of the armour.
Second, Bungie said they are trying to prevent spending tokens on duplicate pieces that just have different colour schemes. For example, Gambit Prime armours are all fused into just the base model - Illicit Gambit Prime armour.
Similarly, you will find unified models for Leviathan Prestige class items that have assumed the base version's looks and Red War Parade armours share the appearance of the armour from the introductory mission, which is no longer available due to being vaulted.
Green and Blue Solstice armours have also been merged into existing models and Purple Solstice armour will get the glows back later on. Year 1 ornaments fall into this category and will be added supposedly around the same time.
Considering that some players spent a lot of time grinding up some of the alternate versions of same-model armour pieces, this decision will not sit well with them but with the state of ridiculous time-gating of the transmog system, many have probably given up on it anyway.