All perfect praise be to Allah, The Lord of the worlds. I testify that there is none worthy of worship except Allah and that Muhammad, sallallahu ‘alayhi wa sallam, is His slave and Messenger.
Ibn ‘Umar, may Allah be pleased with them, reported that the Prophet, sallallahu ‘alayhi wa sallam, said, "Every intoxicant is Khamr (alcohol), and every intoxicant is unlawful." [Muslim and others] Most of the scholars held that alcohol is impure. An-Nawawi wrote, "We are of the view that alcohol is impure, and so is the view of Maalik, Abu Haneefah, Ahmad, and all scholars, except for what Al-Qaadhi Abu At-Tayyib and others narrated on the authority of Rabee‘ah (the teacher of Maalik) and Daawood; both said, 'Alcohol is pure even if it is unlawful, like poisonous plants and intoxicant Hasheesh.' Shaykh Abu Haamid reported the scholarly consensus on its impurity." [Al-Majmoo‘]
If the varnish contains alcohol that has not transformed into a different substance, then, according to the majority of the scholars, the floor is considered impure and the prayer performed on it is invalid. However, it is permissible to spread a pure mat or carpet over the impure floor and pray on it. Ad-Dardeer wrote about the purity of the prayer place:
"The prayer place is the area that comes in direct contact with the body parts of the praying person during prayer. If he is gesturing with his head or eyes in an impure place, then his prayer is valid according to the preponderant view. The same ruling applies if the impurity is under his chest (when he prostrates), between his knees, between his feet, to his right or left, in front of him or behind him, or under his mat. If he spreads a straw mat with impurity underneath it, but the face of the mat on which he places his body parts is pure, then the impurity does not affect the validity of his prayer ... even if the mat moved with his movement. What matters is the purity of the parts of the mat that are in direct contact with his body." [Al-Mukhtasar]
If the ethanol has transformed into a different substance during manufacturing and processing such that it is no longer intoxicant, then the varnish is pure according to the preponderant scholarly view. This is the chosen view of Ibn Taymiyyah and Ibn Al-Qayyim . Shaykhul-Islam Ibn Taymiyyah, while discussing this issue and declaring the view that it is pure to be preponderant, wrote, "This is the decisively correct opinion in this regard; the substances whose prohibition is not stated in religious texts in name or in meaning are not unlawful, nor are they held in the same status as prohibited substances, and there are no grounds for declaring them prohibited. Rather, they fall into the category of lawful things..." [Majmoo‘ Al-Fataawa]
Ibn Al-Qayyim wrote:
"It is inconceivable that the impurity remains despite the fact that its name and description cease to exist (when the impure substance is transformed into a different substance). The religious ruling is subsequent to the name (of the substance), and the description of the substance is connected to the name (if the substance is transformed into another substance, its description changes, and thus the ruling on it changes). The religious texts underlining the prohibition of the dead animals, blood, pork, and alcohol do not refer to plants, fruits, dust, salt, soil, and vinegar as none of them has been clearly stated, implied, or inferred to be prohibited through Qiyaas (analogy) ..." [I‘laam Al-Muwaqqi‘een]
As for your statement, "I also read a fatwa that says that if impurities penetrate an absorbing material like wood, it becomes impossible to purify it," scholars addressed this issue. Sharh Al-Kharshi ‘ala Mukhtasaar Khaleel Al-Maaliki reads, "...Pottery cannot be purified from a penetrating impurity like alcohol, urine, and impure water. Penetrating means permeating extensively and reaching the parts of the pot when it remains inside the pot for a period of time that makes it most likely that the impurity has penetrated all its parts."
Allah knows best.