Utilizing the spacer is the way that Scag designed their decks. This provides more space above the blade without needing to make a longer or taller spindle housing depending on how one views it. Airflow is a key factor in the evacuation of the grass clippings and increasing the distance from the top of the blades to the underside of the deck using a blade bolt and spacer is how Scag set it up.
Nothing wrong with this setup, several other manufacturers use the same.
These machines are lawn mowers and not brush hogs, look at the underside of a brush cutting type rotary machine and you will see the difference. Brush cutting machines turn at a much slower speed utilizing a much heavier blade.
Most modern lawnmower blades turn at a blade tip speed around 18,000 Feet per Minute with the max alowable of 19,000 Feet per Minute by federal safety regulations. When a blade turning at these speeds strikes a hard object nasty stuff can happen!!
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Spindles and housings need to be inspected from the underside of the deck. Blade bolts also need to be inspected and a bent one may indicate that more damage has occured. In a spindle assembly there is the part that turns and thru which the blade bolt passes. With the blade bolt removed, the lower part can be inspected where the blade spacer makes contact. With the deck drive belt removed, the spindle can be turned to check it for running in the center, this usually takes two people to accomplish.