Looking at the original sim, it looks to me to be 100% imperial values you used even though some values suggest that it may be metric (but it is not). Bruce's sim looks to me to be 100% metric which means you will end up with those minute differences (edit: and it actually caught me off guard a bit with the AA guns).
Quickly throwing it through SS gives me this and it looks like you will save half a ton per ship for each refit.
Philomedes, Atlantean Battleship laid down 1931
Displacement:
39,102 t light; 41,462 t standard; 45,962 t normal; 49,561 t full load
Dimensions: Length overall / water x beam x draught
746.23 ft / 732.00 ft x 108.50 ft x 32.15 ft (normal load)
227.45 m / 223.11 m x 33.07 m x 9.80 m
Armament:
9 - 15.00" / 381 mm guns (3x3 guns), 1,687.50lbs / 765.44kg shells, 1931 Model
Breech loading guns in turrets (on barbettes)
on centreline ends, majority forward, 1 raised mount - superfiring
15 - 6.00" / 152 mm guns (5x3 guns), 108.00lbs / 48.99kg shells, 1944 Model
Breech loading guns in turrets (on barbettes)
on side, all amidships, 1 raised mount - superfiring
16 - 3.95" / 100 mm guns (8x2 guns), 30.81lbs / 13.98kg shells, 1944 Model
Dual purpose guns in deck mounts with hoists
on side, evenly spread, all raised mounts
48 - 1.57" / 39.9 mm guns (12x4 guns), 1.93lbs / 0.88kg shells, 1944 Model (=> original sim gives 40mm instead of 40.0mm suggesting it was edited to change it from 39.9mm to 40mm)
Anti-aircraft guns in deck mounts
on side, evenly spread, 10 raised mounts
48 - 0.79" / 20.0 mm guns (12x4 guns), 0.24lbs / 0.11kg shells, 1944 Model
Anti-aircraft guns in deck mounts
on side, evenly spread, all raised mounts
Weight of broadside 17,405 lbs / 7,895 kg
Shells per gun, main battery: 145
Armour:
- Belts: Width (max) Length (avg) Height (avg)
Main: 16.0" / 406 mm 460.00 ft / 140.21 m 13.12 ft / 4.00 m
Ends: Unarmoured
Main Belt covers 97 % of normal length
- Torpedo Bulkhead:
1.97" / 50 mm 460.00 ft / 140.21 m 28.00 ft / 8.53 m
- Gun armour: Face (max) Other gunhouse (avg) Barbette/hoist (max)
Main: 16.0" / 406 mm 11.7" / 297 mm 14.0" / 356 mm
2nd: 3.94" / 100 mm 2.35" / 60 mm 2.76" / 70 mm
3rd: 1.00" / 25 mm 1.00" / 25 mm -
- Armour deck: 6.00" / 152 mm, Conning tower: 12.00" / 305 mm
Machinery:
Oil fired boilers, steam turbines,
Geared drive, 4 shafts, 115,000 shp / 85,790 Kw = 28.18 kts
Range 15,000nm at 15.00 kts
Bunker at max displacement = 8,100 tons
Complement:
1,569 - 2,040
Cost:
£16.048 million / $64.191 million
Distribution of weights at normal displacement:
Armament: 2,176 tons, 4.7 %
Armour: 16,138 tons, 35.1 %
- Belts: 4,240 tons, 9.2 %
- Torpedo bulkhead: 939 tons, 2.0 %
- Armament: 3,712 tons, 8.1 %
- Armour Deck: 6,914 tons, 15.0 %
- Conning Tower: 332 tons, 0.7 %
Machinery: 3,439 tons, 7.5 %
Hull, fittings & equipment: 16,550 tons, 36.0 %
Fuel, ammunition & stores: 6,859 tons, 14.9 %
Miscellaneous weights: 800 tons, 1.7 %
Overall survivability and seakeeping ability:
Survivability (Non-critical penetrating hits needed to sink ship):
68,103 lbs / 30,891 Kg = 40.4 x 15.0 " / 381 mm shells or 10.9 torpedoes
Stability (Unstable if below 1.00): 1.03
Metacentric height 6.0 ft / 1.8 m
Roll period: 18.6 seconds
Steadiness - As gun platform (Average = 50 %): 70 %
- Recoil effect (Restricted arc if above 1.00): 0.65
Seaboat quality (Average = 1.00): 1.11
Hull form characteristics:
Hull has a flush deck
and transom stern
Block coefficient: 0.630
Length to Beam Ratio: 6.75 : 1
'Natural speed' for length: 31.44 kts
Power going to wave formation at top speed: 54 %
Trim (Max stability = 0, Max steadiness = 100): 63
Bow angle (Positive = bow angles forward): 17.00 degrees
Stern overhang: 4.60 ft / 1.40 m
Freeboard (% = measuring location as a percentage of overall length):
- Stem: 31.50 ft / 9.60 m
- Forecastle (20 %): 22.00 ft / 6.71 m
- Mid (50 %): 22.00 ft / 6.71 m
- Quarterdeck (15 %): 22.00 ft / 6.71 m
- Stern: 22.00 ft / 6.71 m
- Average freeboard: 22.76 ft / 6.94 m
Ship space, strength and comments:
Space - Hull below water (magazines/engines, low = better): 77.8 %
- Above water (accommodation/working, high = better): 166.4 %
Waterplane Area: 62,292 Square feet or 5,787 Square metres
Displacement factor (Displacement / loading): 112 %
Structure weight / hull surface area: 200 lbs/sq ft or 975 Kg/sq metre
Hull strength (Relative):
- Cross-sectional: 0.96
- Longitudinal: 1.39
- Overall: 1.00
Hull space for machinery, storage, compartmentation is excellent
Room for accommodation and workspaces is excellent
Ship has slow, easy roll, a good, steady gun platform
Actually the only slightly bigger problems with the designs are the low stability that becomes lower with the additional miscellaneous weights (but that is an issue of the original sim) and the fact that I now realize that you simmed it with a transom stern while the top view of the Philomedes shows a non-transom stern.