So if you have 50 employees that's $5,000 per month, which could be used to pay another salary. Or you could pay your employees that extra $100 directly so they use it whichever way they want.

Employee discounts in retail are usually within company margins for sales and they are limited (e.g. $1,000 purchases per year or so). If the margin doesn't cover these discounts or the system is abused they will get reduced/removed. Likewise, if a startup thinks these $100 per month are better spent elsewhere perhaps they are just being financially responsible.