If you read through the text in the current standard, when calculations are done for the reinforcing strength and area, the thickness and size of repads can be reduced or they can be eliminated, based on results of the calculations. So comparison of your inserts to the tables won't necessarily tell you anything.
Note that the tank should have been built in accordance with API-650 reinforcing requirements, not necessarily repad dimensions.

Do you know the grade of steel in the bottom ring?

IFR,

Unfortunately no I don't. The shell material and thickened inserts material is unknown.

The tank diameter, tank height and shell thickness suggest that the shell material is not API Group IV or above which was my first thought on why all the penetrations were in insert plates. The reason they are that way does not really matter. API 650 allows penetrations to be in thickened insert plates, and they could easily be within the standard. Per Figure 5.7b, thickened inserts should be large enough to swallow the repad size in table 5.6 (although it only shows the vertical axis, I extend that to the horizonatl axis as well). I like to make them the width of a circular repad (Table 5.6 column 5) plus the bevel to make reinforcing area easier to calculate, height similarly computed. The thickness needs to incorporate adequate reinforcing, which would be calculated using the centerline elevation of each penetration, the thickness and material of the neck, the neck projection inside and outside, the design SG, design temperature, corrosion allowance, etc. Again, it's possible that your tank meets all API 650 requirements but you'll have to run the numbers to be sure.

Let me point out too, that for exactly the issues IFRs mentions relative to the design, it is very uncommon to go back and try to confirm a design itself.
It will help considerably if the tank drawings and/or the nameplate are available.
You could spend the rest of your life re-checking the design of everything in a refinery.