It cannot be denied that such complex measures as accountability, which are imposed on municipalities, are completely justified, in my view. They are asked to submit detailed information for a project to be approved and this creates a far greater burden for small municipalities.
That said, the federal government faces the same dilemma when dealing with indigenous communities, for example. In some cases, there are programs to help indigenous communities increase their capacity in that regard.
It is easy to envisage federal or provincial assistance for municipalities. This would help them acquire the capacity, with their staff or third parties, to meet the infrastructure program criteria. The example you gave is probably quite common. Many municipalities and governments definitely find themselves in the same situation. It is the norm for small organizations to have one person who performs many roles.
I have a great deal of empathy for the chief administrative officers of small municipalities. They have to meet a set of criteria, fill out many documents, collect information, and liaise with elected officials and public servants at various levels of government. That is probably an important factor in the delays experienced or the time taken by certain municipalities to meet the requirements.