DND 3.5E HP Damage – Understanding HP Damage and Constitution Damage

No.
Ability modifiers are applied to damage, but half-level isn't. So, in your example, the Flames of Phlegethos would inflict 3d10+3 damage.

Half-level is applied to attack rolls because they are ability checks. As a more general rule, feel confident to add half you level to every d20 roll except saving throws and to every static number which usually stands against a d20 roll (like defenses).

When you polymorph into a troll, your hit points do not remain the same, they are adjusted for your new CON. See this Rules of the Game article.

As other CON-affecting effects apply, they also modify your CON, so yes if you get CON drained your hit points reduce.

When you change back, your base CON goes to its original but other effects (like the drain) do not go away and you now have a lower-than-your-usual CON (this can kill you if you're not careful).

Now, in a case like Alternate Form where a CON change doesn't change hit points, the RAW is unclear and also fairly problematic. It doesn't really make sense to be immune to CON drain but it also doesn't make sense to kill you fast via CON damage/drain because your non-CON-augmented hit points go down. What I would do in my game is let CON damage not affect hit points until it goes under the underlying characters' CON. So in a form with CON +8, you could get 8 points of CON damage before having to worry about it. But actually, I would probably just strike the "CON change doesn't change your hit points" rule as being pointlessly fiddly.