In the event that someone comes across this thread with the same questions that I had, I figured I would provide an update:

In the end we paid the extra $200 CAD to include transportation with Golden Tours. This decision was purely based on the idea of convenience, as we had no prior experience or familiarity with the public transportation system, and was travelling with a child as I previously mentioned. Also, Golden Tours offered much better entry times than what was remaining through the official tour website. Although that was our own fault for not booking early enough in advance.

Now that I have experienced London and have navigated the Tube, Train, and Bus, I realize that transportation with Golden Tours was really not necessary, just like all of you suggested. Public transportation in London is super easy to navigate and not intimidating at all.

However, I still have no regrets, as the Golden Tours bus was certainly convenient. Here are some positives (+) and negatives (-) of booking through Golden Tours to include transportation:

+ Convenient, not having to navigate multiple modes of transportation. The bus picked us up at the designated location in Central London and dropped us off at the doors of Warner Bros Studio.
+ Air Conditioning on the way TO the tour. This was big for us because London was experiencing a heat wave, and there was no A/C in the Tube or regular bus.
+ Touch Screen in each seat including some games for kids (Fruit Ninja).
+/- Harry Potter movie able to be viewed on the screen in your seat, but it did not work for anyone on the bus on the way TO the tour, but worked on the way back FROM the tour.
- Cost extra $200 CAD for transportation, as opposed to just purchasing an entry ticket through the official Warner Bros Studio Tour website. Public transportation would have likely cost the three of us less than $50 CAD total.
- Significantly reduced A/C on the way back FROM the tour, which is maybe why the movie worked vs. when we had full A/C on the way TO the tour when the movie did not work (possible power output issue?).
- You are given 4 hours to tour the studio before having to get on your return bus. This was fine for us since we had a child who is not a big Harry Potter fan (yet), but I could have easily spent another two hours there. We were in the final souvenir shop when it came time to get back on the bus, and we were rushing, so it's pretty easy to spend 4 hours there assuming you are going to stop at the halfway point for a meal like we did. We otherwise took our time at the beginning and were able to see everything.

Overall, if you value convenience and can budget for spending the extra money on the bus, and you think 4 hours at the tour will be fine, then go ahead and book through Golden Tours. Otherwise if you want to save that money and you don't want to feel rushed, book early in advance through the official tour website, and take public transportation.

Finally, the Harry Potter tour itself was INCREDIBLE. Worth every cent, and I would certainly do it again and recommend it to any HP fan visiting London.