How are stellar elemental abundances quoted?
First of all, your first question.

This source clearly state that Values are given in the usual logarithmic (dex) scale, for the same formula that you quoted (similar job).
It is a bit tricky as the article "explains" the values, but you have to pay attention to the exact definition.

I think it is better to work out with an example. Let's take the He. 

Good enough, you can better read the paper from here.

From the table, we have $A_{el}=10.93$. This is the abundance of He relative to H (in logarithmic scale).
From this you find out that $\frac{N_{el}}{N_H}=0.08 = 8\%$.
Indeed the work confirms this value (see the last page).

What you quote as about 25% He, is what they call abundances by mass of [...] Helium (Y), which means $Y = mass\ of\ Helium / mass\ of\ Hydrogen$, and this is indeed about $25\%$.