What Silver said I am talking about the current armor. The newest cruiser would be around a Mass: 480,000 tons and with a good integrity can carry 480 tons of armor but that armor is worth only 0.26 points each or 0.40 at standard. That is not a lot of points because the armor is spread out over a larger area. The thing you seem to be completey missing is that mass means jack the points are all that matter here. That comes out to only 28 points on a single area or less an force to concentrates on one area which is how naval battles are fought will breakthrough because the armor isn't as thick as it would be on a smaller ship.
Now lets go with dropship of assault size which would be about 2000 it would only take 2 tons of armor to get the same kind of points as the cruiser. A dropship get 10.56 points per ton on primitive and 16 on standard. So while the Cruiser does have more armor it has less points. But that is with BT construction and designs that require that everything be so full of redundancy and thick because of the technology they are very tough and survivable with ships being rebuilt all the time. Helghan Ships on the other hand do not work like that we don't need all those extra systems because we have technologies that make them irrelevant so they are more fragile in comparison. It comes down to design philosophy.
Right then - I got sufficiently fed up with you trying to sell me the idea of Warships actually being less protected than a random dropship for any given armor location that I went and downloaded megameklab and tore through it to try and figure out what your malfunction was. What I found was that MML builds warships and assigns armor/weapon values using Capital-scale points, which convert to Standard Aerospace/Battlemech/etc points at a 1:10 ratio that you haven't accounted for.
So running the same numbers you gave for fully upgraded Cruisers of 480 tons of standard Armor, autoallocation gives point values of 49, 41, 36, and 25 for the Nose, front sides, rear sides, and aft facings. I multiplied by ten to convert to standard points and dug through Sarna to see if I could find examples of assault dropships or pocket warships that listed armor type and tonnage and give a serious comparison.
All of these are using the same autoallocation system, to make sure we're comparing apples to apples and because sarna is usually pretty spotty about specific allocation schemes.
Upgraded 480k ton Cruiser, with 480 tons Standard Armor - 490 points nose, 410 points front sides, 360 points rear sides, 250 points aft.
4500 ton Achilles assault dropship, with 60 tons standard - 302 points nose, 254 points sides, 206 points aft.
4000 ton Pentagon assault dropship, 75.5 tons standard - 380 points nose, 319 points sides, 258 points sides.
18 000 ton Aesir fighter carrier, with 90 tons Ferro-Aluminum - 216 points nose, 222 points sides, 181 points sides.
16,000 ton Nekohono'o assault ship, 57 tons Ferro-Aluminum - 211 nose, 180 sides, 147 points aft.
12 000 ton Titan class Monitor, 80 tons Ferro-Aluminum - 342 points nose, 289 points sides, 235 points aft.
1900 ton Leopard Pocket Warship, 54 tons Ferro-Aluminum - 310 points nose, 262 points sides, 213 points aft.
Average number of points of protection for assault dropships and pocket warships, ~294 points nose, 255 points sides, 207 points aft. In direct comparison, the most vulnerable points on the Cruiser ought to be ~25% tougher than the weakest points on an assault dropship, with the better protected regions being 40%/60%/66% better protected.
For funsies, I ran the math for what 480 tons of Primitive Armor gives - which turned out to be 340 points nose, 290 points front sides, 260 points rear sides, and 180 points aft. That's actually pretty close to the numerical values I dug up for assault droppers, so it turns out despite being lower tech the Hasta-class Cruisers ought to be very competitive in toughness compared to IS dropships.
Circling back to the original point rather than just the numbers and math proving it,
No, fully upgraded our cruisers would have a serious advantage over assault dropships, because they have the size/mass/armor allotment of destroyer sized warships. It's why they are currently a match for combat dropships despite being slow as balls and having low quality armor in comparison. They wouldn't hit any harder than an assault dropship when fully upgraded, but they'd have a lot more armor to absorb hits with.
At full the armor with be at full but we still wouldn't be overpowered on the assault and pocket warships.
Yes, being 50-60% better protected is a serious advantage - literally the numerical difference between standard and primitive at some points, only based off of bulk and tonnage instead of tech differences.
And no, the Helghan design philosophy isn't to ignore armor or physical durability in favor of other technologies - the Cruiser, the MAWLR, and the Helghan Overlord-class dropship are all described as heavily armored. The fact that these things can't stand up to ISA weapons all that well is specifically called out as being explained by either poor materials science going into the armor (which doesn't matter when those things are being replaced by IS materials science) or just the ISA weapons being that good in comparison (which also doesn't matter because those aren't the weapons in question).