The development case
The strongest argument for reserve teams in a professional division is that youth football stops teaching a player anything once he is good enough for it. Facing experienced professionals who are playing for contracts, in front of crowds who care about the result, exposes the parts of a young player's game that under-nineteen football flatters: decision-making under real pressure, physical duels against grown men, the discipline to hold a position when losing.
Countries without that intermediate step tend to lose players in the gap between academy and first team, or to send them abroad on loan and hope. A third-tier reserve side is an unglamorous solution to a genuine problem.
The competitive objection
The objection is equally serious. A club fighting relegation may face a reserve side whose selection depends on the parent club's midweek fixture, so the opponent on one weekend bears little resemblance to the one another club faced a month earlier. That is an unfairness the table cannot absorb, and it sits uncomfortably in a division where results decide whether small clubs survive financially.
There is also an atmosphere problem. A fixture against a second team rarely draws a crowd, and for clubs dependent on matchday income, that is a measurable cost of somebody else's development plan.
How the balance is attempted
The usual compromises are structural: reserve teams cannot be promoted into the division their parent club occupies, cannot enter the main cup competition, and often receive reduced or no share of certain distributions. Those rules do not remove the selection-consistency problem, but they do prevent the worst outcomes, such as two teams from one club competing in the same league.
Whether the trade is worth it depends on what a third division is for. If it is primarily a competition for independent clubs, the objections win. If it is also the top step of a development pyramid, the current arrangement is a defensible, imperfect answer.