Outside of honoring those specific instructions that you implement on the front end, they have full discretion to buy and sell whatever they see fit.
Typically, in a separately managed account, the fee that you pay as an investor includes transaction costs, so there's no incentive for the money manager to run up transactions on you.
Wall Street has lost business to fee-based advisers in the last several years.
There can be more moving parts to them. It does require that somebody keep up with it.
There's better tax control inside a separately managed account.
The financial adviser's job is to marry up the proper money manager's strategy with your unique individual needs as an individual investor and your tolerance for risk.