Alright, out of sheer boredom and a never ending desire to find out the true reason as to why Bert & Ernie's Loch Adventure does not have a drop compared to the vastly superior RR, I have come to two possible conclusions.
#1. This makes the most sense logically, but as other forum members have said, the ride was a pain in the rear to operate with that pesky little lift. It seems like due to it's short length and the weight of the themed fiberglass boats combined with the weight of the passengers, that it would put a lot of strain on the actual chain making it a challenge to send them over the top. I could be wrong, as this was a very long time ago, but I even remember an attendant sitting near the lift to make sure the boats would successfully clear it, despite it's short height.
#2. This is something that I just recently noticed, but there is a significant difference in size between the RR and Bert and Ernie's Loch Adventure boats. The BAELA boats, something about that just doesn't roll off the tongue as nicely, had additional material added to the side to make it easier to enter and exit the boats, which also increased the weight.

Assuming that these are the same boats from Riffle Rapids, and they just received new paint jobs based on the nearly identical design, there's a significant lack of the side material found in the older version. I've attached an extremely blurry photo for reference.

Tampa actually still operates their kiddie flume with the drop, and as you can see in this photo these ride vehicles don't have the additional side material found in Williamsburg and are still the original slimmer model with a different thematic shell.

With the weird shaping of the FOF ride layout, specifically the part where the flume opens up near the awkward fountains that don't get you wet, but just go over guests, it makes me wonder if this ride was originally planned to have the drop. Tampa still somehow manages to use their original flume, but for some reason Williamsburg seems to have deemed it not worthy of operation. Even in the original concept art for FoF, a drop can be seen in the back right corner of the layout.

As a kid, I really enjoyed Riffle Rapids with the slow turn underneath the bridge past the foliage, the clanky crawl up that slow lift where you would wave to the attendant, and the satisfying splash followed by a turn around back to the station. B&ELA just seems lifeless in comparison with it's cartoon cut out castle, flat ride layout, and practically empty in-field. Most guests have probably even forgotten that RR ever existed, and many probably never even knew of it's existence tucked in the back of LOD underneath the main tree house.
I find it interesting that B&ELA seems like it was planned to have a drop, has the space for a drop, and just doesn't have a drop. I wonder if they added the extra material to make the ride more accessible, without realizing that it wouldn't be able to properly go up the lift? Or, if they just decided it wasn't worth the effort to move the already troublesome lift mechanism? Anyways, it's just a kiddie ride, and RR is merely a memory of the past in my mind, as fans it's our job to try and overanalyze every single aspect of the park good and bad, and as someone who's been interested in the park for a very long time, there's few things left that are left unanswered, and this ride is one of them.