You are right, more media will restrict the flow. You also have to look at the area available as well.
With full media in the center of the baskets, the area in which water can "flow" is reduced. The only areas the water can flow will be between the all the media. This will cause the flow to be redirected in many different directions and also cause some of the water to "stall". Since the center of the baskets are pretty small and with lots of media this can create a high velocity of flow around all the media but velocity is directly related to pressure which in this case would be restriction of flow. The more media there is the more of a pressure drop there is meaning more vacuum which means there is restriction. Velocity is good as long as there is a balance since velocity can actually help the water flow through the restriction since it now has lots of momentum. Problem being, we don't want high velocity through the bio media otherwise it will take twice as long for the bio to consume the toxins. Contact time is a very important factor with bio media which is why you want so much of it to increase the contact time. With lower velocity and more media, this should help drastically.
Have you seen the Fx5 vs Eheim 2080 Comparison? The Eheim with its 12L of media, large area and slower flow cycled a couple days sooner than the Fx5 with a faster flow, less area and only 6L of media. Now, try to think of how much faster the Fx5 could have cycled if the flow was reduced to that of the Eheim 2080. It would still take longer but should not have taken anywhere near as long as it did since the contact time would be increased with the slower flow. Just to get an idea of how much more flow there was in the Fx5 compaired to the Eheim 2080, the Fx5 flow 207 GPH MORE. Thats 0.46 cubic feet more per minute. Remember thats 12"x12"x12" water colum. In a 6.5" diameter water column thats about 2 feet per minute more (Online Calculator) with a total unrestricted flow of 5 FPM at 525 GPH. Doesn't seem like much and it actually is not untill you add the media which will restrict the flow more and cause it to speed up and with less volume output. So lets throw a number out there and say that with full media, that is equal to a 3" diameter column (remember throwing a number out there). That brings it up to 9 feet per minute more with a total flow of 24 feet per minute at 525 GPH.
The last part of that paragraph is not factual for our filters just an idea of how the media could effect the flow.
With this modification, you are drastically increasing the area in which the water can flow (more open areas around media) decreasing the restriction.
This could drop the unrestricted velocity of flow down to 1 FPM at 525 GPH. The "unrestricted" part is very important. Thats without anything in the filter. No baskets, no egg crate, no foam, nothing.
So yes you are correct but just can't forget about the increase in area that has been given.