"The spell is being cast on a wizard that currently resembles a troll, not a troll. "
Absolutely wrong. A character who polymorphs into a troll is a troll for the duration of the spell, not someone who merely resembles a troll.
There is nothing wrong with the way the character wants to use these spells.
Polymorph self changes the character into a troll, with average ability scores as follows:
1. Strength 23
2. Dex 14
3. Con 23.
The character keeps his/her int, wis and cha scores.
There are no combat bonuses per se, as the character's base attack modifier remains the same. Granted, the strength modifier of the troll will definitely improve attack and damage bonuses to a total of +6, but these are bonuses based on a natural, un-enhanced ability score. They are not enhancment bonuses.
The improved constitution score improves the character's fortitude save, but it does not provide the +6 per level con bonus to hit points. The character's hit point total remains the same. The fortitude save bonus is based on a natural ability modifier as well, and it is therefore also, not an enhancement bonus.
If the wizard polymorphs into a troll, he/she can still cast spells, because all that s required is the ability to speak and to possess humanoid type hands, which a troll does possess. So, the character could then cast Tensor's Transformation to turn into a fighter for the duration of the spell. Thus, one spell changes the race of the recipient and the other spell changes the class of the recipient.
TT grants 1d6 additional hit points per level, a +5 Fortitude CIRCUMSTANCE bonus, which does indeed stack with the +6 natural ability bonus from being a troll. TT also makes the transformed wizard proficient with all martial and simple weapons, and it grants an ATTACK bonus of 1 for every two caster levels.
TT also provides an ENHANCEMENT bonus of 2d4 to strength and dexterity, which do indeed stack with the natural ability modifiers a troll would get. However, if the character possesses a belt of giant strength or gloves of dexterity, or if he/she is under the effect of a cat's grace or bull's strength spell, the enhancement bonuses from TT would not stack with the enhancement bonus of those spells or spell effects. The character would have to take the greater of the effects.
Change self could certainly be used to disguise the PC, granting a +10 circumstance bonus to the character’s disguise check. Whether he/she is polymorphed is irrelevent.
If it were not possible to stack Transmutation spells, as you seem to be inclined to believe, then it would not be possible to allow a character to enjoy the benefits of a Bull's strength and a Cat's grace, at the same time, since both are transmutation spells. However, we know that this is not the case. Granted, it is not possible to stack "like" bonuses, but as I described above, the bonuses received from Polymorph self are natural ability bonuses, while the bonuses from TT are both CIRCUMSTANCE and ENHANCEMENT bonuses.
It seems to me that the player in question, has developed a very nice combination of spells. It would not be right to hamper his ability to use the spells.