It's a useful budgeting tool. It's not like there is one "government bank account" that every agency and bureaucrat shares.
In the US, agencies can end up with surplus cash (either taxes were higher than needed, or budgets were off, etc). Agencies will buy T bonds with this excess cash to transfer it back to the Treasuries general fund, so it can be reallocated. The T bonds that the agency now holds are far from "meaningless".
From a thousand foot view, the government is one homogenous entity. But that perspective breaks down pretty quickly in the real world. It's pretty easy to find Intragovernmental debt stats and subtract that from the total, if you are so inclined.
Usually, people are concern with the total liability of a government. You can't dismiss intragovernmental debt in this calculation.