Or are you complaining about the AC/5 not being able to get a penetrating critical hit roll against BAR/5 armor? Even though Autocannons are "superior" to Rifle Cannons?
Bingo! That's the main gripe. Remember, it's not just the AC/5 at stake, though. This also includes the Medium Laser, and the LRM's 5-point clusters, as well. All that jazz you cite about being more superior but not good at Penetration fails as a logical argument when it comes to historical justification for the weapon's large proliferation.
About the complaint of units only have a single BAR and the suggestion of Patchwork armor. That sure seems to be what you were wanting but whatever. Again, whatever works for you. 
When combat equipment came out with the BAR system and Support Vehicle Construction Rules under FanPro, (what went into the first few errata-free versions of Total Warfare) I did play around with Patchwork armor to get different crit thresholds. It was okay, at first. I still had issues with the short ranges, and I knew what that meant. So, it would require some house-rules or loose interpretations of AeroTech Low-Altitude ranges to work to begin to emulate different levels of tech.
But, then some people pointed out that BAR has more to do with the failures of the materials involved in the armor, and not anything to do with armor thickness. (That happened to be Cray.) And, other people pointed out that BT damage does not reflect penetration, considering what it does to armor. (CannonShop, I think.) And, having rudimentarily studied 20th and 21st armored combat, the munitions involved and the final effect, I get why.
I honestly enjoyed TRo 1945. But, when it comes to emulating true modern armored combat, it has some good things, but it has some bad things, too. So, it turns out to be 'okay' in my book. I'm more okay with the BAR system in it and at the RPG level. But, both are at a completely different damage scale, and that's why it's okay in using each one.
Edit: And, I'll leave it there, as per the OP's request.
New question for the group: what balance issues if any are presented by just ditching the -3 damage penalty?
When answering set aside this idea that Rifle Cannons are using hundreds of years old technology. Forget about TRO 1945.
Instead let's just examine their game stats: weight/range/damage/ammo per ton.
Looking purely at that - are they balanced as an alternative to the Autocannon?
Well, I have a counter-question to you. Do you see AutoCannons as single-shot? Or certain brands as single-shot?
Because it has been argued that ACs are a simple change of metallurgy and propellant. I disagree in that I see all ACs as firing multiple shells. There may be some exceptions in a TRo entry, somewhere. But, for the most part, a lot of the weight gains have more to do with 'recoil compensation'. That's not something required for a single-shot gun.
Rifle Cannons are single shot tubes. You can point to any tank the fields a single-shot tube, and the fact that each round is generally selected and fed into the barrel. It's not fed directly from a magazine or belt. Most tanks have a variety of munitions to choose from, loaded for expected encounters on the mission.
HESH rounds are used for Building demolition and scrapping lightly armored vehicles, like cars and trucks.
Heavy Metal Darts are used for penetrating heavy armor. You'll see different variations for different armors.
Cannister Rounds with flechettes or grape shot bearings are great for peppering infantry, and maybe Air targets.
So, why are the cannons having their stats limited to one range band and damage profile for the barrel?
APFSDS darts are going to have a different range and damage profile than Self-Propelled Squash Head rounds versus the 'Grape Shot' round.
Being able to have access to different rounds per shot, instead of a single hopper dedicated all to one kind, is one of the things I know I plan to implement for my use of Tank Rounds.
And, for those concerned about the powder in a casing, there are ways around it. The idea of a self-propelled round kicked out of a casing using said updated powders would be one way to keep the barrel structurally sound and use the new hotness. It may seem a step backwards, since a two-stage propellent, one being a rocket block at the end of a dart, had been discarded, but tried, historically. It was usually used in conjunction with a HE tipped round which was kinda slow and heavy and not very aerodynamic.
If you look at the ammo options as the source of the stats, then you don't need to have the stats applied strictly to the gun.
Honestly, I look at the -3 is representing the old-fashioned long rod penetrator, which is an ammo type. It's a tiny dart whose sole purpose is to poke a big hole through a plate of armor. The donut-hole sized piece that gets dislodged is then supposed to bound around in any number of small pieces, wreaking havoc on senstive motors and motor-controls and whatever might be nearby.
Standard BattleTech Armor has a second layer with a ferrous carbon weave that stops that spalling effect. So, not only is the round too small to properly represent a full point of damage. Then, you take away it's crit-making potential simply due to the nature of the armor, and yeah.
But, I imagine that you might get the long-rod penetrator up to doing full damage points if it is flung faster. If you use the space range bands, BattleTech Weapons can be
very fast. Like 'dozens of -' to 'a couple hundred-' kilometers a second fast.
I'm not exactly sure that the long-rod can be saved as a single shot munition. But, the single-shot tube doesn't have to be limited to that style of munition.
That's my food for thought.