Rules as Written
But what about spells, like Telekinesis?
Telekinesis reads:
Make an ability check with your spellcasting ability contested by the creature's Strength check.
The rules on Spell Scrolls reads:
The level of the spell on the scroll determines the spell’s saving throw DC and attack bonus
According to the written word, the ability check would be made with your spell casting ability, since the rules do not replace this use in the specific rules for spell scrolls.
Intent and Reasonable Rulings
It is impossible to gather if this was a mistake they didn't care enough to fix, or if this is the rules as they intended.
It would not be unreasonable for a DM to rule that you use any of the following:
- the spell attack modifier on the table
- the spell attack modifier from the table minus a constant value of 2 (the base proficiency bonus at level 1)
- the spell attack modifier from the table minus your proficiency bonus
As long as the ruling you make is applied consistently, all of those would be within bounded accuracy of 5e. And, given the relative rarity of scrolls in most campaigns, none of those would be game breaking.