All sorts of "shallows" in the game are messed-up, such that any water shallower than say 50 foot can lead to issues with the bigger ships. In Stock, look in just about any harbor, and you will find ships spawned into the "mud", or "banging" on the bottom, even though you might zoom-in with the external camera, and see that there is a good 10 foot beneath their keel. I don't know if that has to do with the "detection" area for a "magnetic pistol" torpedo or what, but the ships "hit bottom" before their draft figures say they should. With that, I think Truk and a few other atolls like that were avoided by the devs.
Carotio did a "terrain" mod for Truk years back, which was included in RFB and TMO (??), and that was re-worked in FotRSU. One thing also about the area, is that it is "tight quarters" in there, and a two-column convoy cannot go in, and come out the other side, without losing some of its 'contents' on the way, such that some of the ships will run aground, or collide with other ships, both in its own group, and in others, so it can be a mess in there, even with Carotio's mod. But you should find that RFB 1.5 & 2.0, TMO 2.5 (and previous - and along with RSRDC) and FOTRS and FotRSU all have a re-worked Truk, apparently mostly based upon Carotio's version. I think (warning: biased opinion) that the FotRSU version is the best, of course...
There are minefields and anti-sub nets around the atoll in most of the mods, in an effort to prevent harbor raiding. I'm sure there are other such mods that do a re-working of the area, and I am thinking that when Carotio did the mod, it was for stock, which would work in GFO. Just read his documentation... ?? - I found the old thread:
Carotio Truk Corals Harbours Cities Locations, but unfortunately, the links to his pix and apparently the download also, are broken. However, one more click, and I did find the
Carotio_SH4_TrukCoralHarbourCityLocations download, thanks to Lt commander lare...