ownership and structure are what divides them - operational funding to some degree although the gap isnt as massive as it once was.
NPL clubs, don't have an owner, they are not for profit community sport clubs, they generally have all age teams for both means and womens, a council ground (with some exceptions that own their own land and stadium) and a senior mens and womens team funded by spopnsorship and corproate events mainly (very small match day income)
Aleague clubs are owned by someone or something and pay a licenst to operate in a closed off league and use a particualr geography, set of colours and franchsie name allocated to them by the APL. Some of them ahve some underage mens teams (not girls though apart from seniors) and they call these "academies" for some reason? They all play at council or governemnt owned grounds for exorbitant rent and
senior mens and womens team funded by sponsorhsip, a rapidly diminishing broadcast deal and the generosity of loss making ownerships groups. (They also have a very small match day income)