The glass bottle that Lex took out was only a very mundane glass bottle. It was not made from any spiritual material, nor did it have any mystical abilities. The reason Lex took this out first was because he wanted to get an idea for how quickly the liquid worked, and if it worked on ordinary materials as well, or was it restricted to living beings.
In scientific terms, if Lex were conducting an experiment, then the glass bottle would be the control. Once he had an understanding of how the liquid, which Lex had started to call Holy water temporarily, behaved, then he could find a suitable container for it..
Using his spirit sense, he grabbed the bottle and lifted it into the air. Slowly, so as to not cause a splash, he dipped the bottle into the Holy water and filled it to the brim. Then he lifted the bottle up in the air, holding it directly above the pool in case the bottle also dissolved.
