Fabric choice isn't an alteration as I see it - unless you're attempting to perfectly replicate an extant costume, like a historical piece or a live-action costume, fabric choice is merely part of interpretation, not replication.
When you're aiming for making a replica of a costume, where accuracy is important, if you have a reason for altering or deliberately deviating from the reference material, EXPLAIN IT. Comfort and modesty are perfectly good reasons for changing something, and judges will understand as long as you state that you deviated on purpose and this was your reason. Extrapolating from bad art, nonexistent or inconsistent references, etc, is also a good reason. We just want to know your thought process and decision-making, because part of what makes a good costume is making good choices, not only for the end goal (getting as close to the reference as possible) but for your own skill level, comfort, and aesthetic appearance. And we all know that sometimes references can be wildly inconsistent, so point it out. Explain your process, why you decided to do what you did. This also goes for combining two sources into a single costume. It's not like it's never been done before, but the judges need to be aware that this is what you're doing - if you say nothing and blindside the judges with a costume that looks nothing like the reference picture you just handed them, they have no choice but to wonder why not and possibly overlook you for awards.
It's not so much that you get "points off" for inaccuracy or other failures. Those of us who do use points systems (which I honestly encourage for speed and ease of use) may look more toward rewarding excellent work versus docking for sub-par work. I don't know how other systems or judges do it, but I generally look at the overall picture rather than saying "oh, she forgot a line of trim, that's minus one point from accuracy!" But I do give lower numbers to those who really have no good explanation for why their costume deviates from this picture they just handed me.
Founder and President, Madison Area Costuming Society, a chapter of the International Costumer's Guild
Strange Land Costuming - www.strangelandcostumes.com