Question about iLevel

Does the iLevel actually make a difference? For example, if I have two chest pieces with the same stats, one ilvl80 and the other ilvl90, will I take less damage in the higher one? Or are stats all that matters

Stats are all that matters, but normaly items with higher ilvl have better stats.

Technically it really is the stats on the item that matter. The item level only represents that an item has a higher value of base stats on it.

For example the allagan weapons are being raised from ilvl 90 to ilvl 95 with the patch next week.
This means that the stats already on it or perhaps even the weapon damage will be very slightly raised than its current ilvl 90 version.

Currently - the only situation where iLVL have any importance is the materia as it determines what materia level you can meld to it as well to which materia level it will be converted but as we have no lvl 5 materia in the game right now (leaving aside legacy) this is hardly a factor once your reach iLVL 55.

currently ilvl determines the stat-caps for an item, and the highest level materia that can be melded on to it.
Armor type determines it's Def/Mdef values.

Items that share an ilvl tier will have different stats on them (generally)
Str / Vit / Parry / Determination
or
Str / Vit / Accuracy / Parry

things like that, so your choices across a shared ilvl on items is not based on primary stat/def but on which secondary stats will help you the most.