The issue with this is that PayPal / Google Pay / Apple Pay etc will always incur a fee, so if you put £100 in your FT account, you would lose one or two percent as a fee. So Freetrade limit it so that they don’t lose too much money (by eating that fee themselves).
I agree it would be nice to have unlimited easy payments, but I sadly don’t think it’s going to happen (unless that fee was calculated, displayed, and charged alongside your deposit amount).