Into the Storm is silent on whether Starship Component Upgrades should use Table 9-36 as the Scale modifier, therefore the RAW must be interpreted as using the standard Scale Acquisition Modifiers.
Really? I thought Into the Storm was pretty clear on this.
Upgrades are purchased in the same manner as any other
Acquisition, and can be obtained for any ship. There are
bonuses for Craftmanship for upgrades. However, although
a player may only purchase one starship upgrade per
Acquisition Test, there is no bonus for doing so. Essentially,
the only modifier to an Acquisition Test to purchase a ship
upgrade is the rarity of said upgrade and the craftmanship of
the upgrade. - Into the Storm, page 162.
To call something RAW, you should start by reading the rules as written.