If you can fit the external pickup system, then use it. No downsides IMO.
I've been running that same pump w/ a stock Melling pump cover on my 572" hemi for many years w/ no issues. I did "port" the cover to help the flow. I used to have the Milodon cover for a remote filter for a long time, but got tired of the extra plumbing and clutter, so I put on the normal cover and I'm much happier w/ it.
CHIP
'70 hemicuda, 575" Hemi, 727, Dana 60
'69 road runner, 440-6, 18 spline 4 speed, Dana 60
'71 Demon, 340, low gear 904, 8.75
'73 Chrysler New Yorker, 440, 727, 8.75
'90 Chevy 454SS Silverado, 476" BBC, TH400, 14 bolt
'06 GMC 2500HD LBZ Duramax
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