“For federal employees, employee counts are the on-board "head count" as of the end of the report period.” What is this sentence talking about?

See a translation

Federal employees = Those who work for the government
Employee counts = Number of people who work in a given department
On-board = Currently working
Head count = The number of people (named for the practice of counting "heads" when people are sitting, such as a teacher counting how many of her students' heads are visible as she walks up and down the aisle)
Report period = The time over which the report is being generated.

So it roughly translates to:
"For those who work for the government, the way we report the number of people working in each department is to count the number of people who are currently working at the end of the time we are analyzing."

In other words, if the report period runs from January 1 to May 31:
January 1: The department has 100 employees
January 16: One person is fired
February 4: One person is moved to another department
March 16: One new person is hired
April 3: One person quits
May 9: Someone is promoted out of the department
May 29: Another new person is hired
May 31: The department has 98 employees

Then the number reported is 98 because that is the "head count" at the end of the report period.