I've never encountered any compelling rationale as to why/how that standard emerged.
Market terms for a seed round are either 1) a priced round, or 2) a SAFE or note with a cap and a discount. 20% is a typical discount. A typical cap, in Silicon Valley, would be $4m-$5m on the lower end (idea or prototype phase, little or no market validation) up to $8m-$10m on the higher end (product is live in the market, has decent usage, and perhaps $25k-$75k MRR if you're b2b). There are also outliers that are >$10m cap -- usually those companies have exceptionally strong growth or founders.
In practice, SAFE/note discounts don't come into play that often but caps do. That is, next rounds are usually significantly higher than the cap (and the discount doesn't apply).
I paid closing costs when I bought, and as my realtor said, it's like free cable. It's not a massive savings but it's free cable every month.
The rationale, from the VC's perspective for the company paying for a priced transaction is the same. Really this is a way of making the LPs of the fund pay for the transaction (i.e. their money given to the company to pay the transaction) rather than the VC having to pay transaction expenses out of their fees.