I've been checking the rules online and so far what I understand is that the Unique restriction only takes effect when putting cards into play or taking control. Overlaying is not considered being put into play, right?
Taken from the rules page: http://rules.l5r.com/Ivory_Comprehensive_Rules
Experienced: Some Personality cards have the Experienced keyword, which is sometimes followed by a number representing the Personality’s experience level. A Personality with Experienced and no number has experience level of one. A Personality without Experienced has experience level zero.
Any number of single Personalities with the same title but different experience levels may be included in a deck.
During the Dynasty Phase, a player may bring an Experienced Personality into play normally, or may overlay him onto one of his or her Personalities in play with the same title but lower experience level. When overlaying, a player does not need to meet Honor Requirements or pay costs, but does need to meet other requirements and restrictions, including Loyal (p. 56).
An overlaying card replaces its less experienced version without entering play, and the less experienced card is removed from the game without leaving play. On overlaying, the new card keeps all states, ongoing effects, attachments, and tokens of the old card, and is considered to be the same card.
Unique: A player will not bring into play or take control of a Unique card if he or she already controls a Unique card with the same title (but see Experienced, p. 51). If a player takes control of a unit with a copy of a Unique attachment he or she already controls, discard the new attachment.
So for example:
A deck can have three copies of the basic Daidoji Tametaka, one of his exp1, and another of his exp2. A player can also control any number of copies of the basic Tametaka and only one of either of his experienced versions because both are Unique. Now, if I had a basic Tametaka and his exp1 in play, can I overlay the exp2 onto the basic Tametaka thus having both Unique versions in play?