The problem is your intake is capable of taking in more water than it needs to... so impeding the flow (to a point) is not a problem...
When you have an intake that can handle 1,000 gph... but the pump only puts in 500 gph... the intake is starved for water and thus sucks air...
Balancing the intake with the intake is important when it comes to silencing a drilled tanks intake. Naturally if the pump moves even slightly more water than the inake overflowing will occur. So avoid this at all costs.
Keep in mind that over time the prefilter on the pump is likely to get slightly clogged which will slightly reduce to pumps flow. The pump will never push more water than it will when it is brand new (under normal usage, naturally purposfully manipulating it may result in greater flow).
It is necessary to take precautionary steps to prevent waste or debris from clogging or otherwise hampering the intake. But this is true in any overflow intake situation.