If your company manager account is a manager for the relevant client accounts, you would just need to authenticate as the manager account using your developer token, client id and secret. This gives access to the Ads data for all clients linked under the manager account.
E.g. calling Google Ads API CustomerService > ListAccessibleCustomers returns a list of customers accessible to the authenticated client.
Further to comments where you say you will be creating a console app:
The link in your question says use a desktop application if:
You're managing all of your Google Ads accounts using a single top
level manager account. You're a first-time user, or want to get
started quickly with the simplest setup. Your app will only
authenticate Google users from one machine.
So using a manager account which links the required client accounts would be required in this case. See OAuth desktop application flow.
If you used a web application, the clients could log in and your app could read and store their refresh token in a database to make future calls to the api for their account.
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