「インターネットの安全のための仕事などをするIPAによると、銀行やクレジットカードの会社など、本当にある会社の名前を使った、うそのメールが多くなっています。」
In this sentence, the "main" verb is 「います」 or the whole verb phrase 「多くなっています」 at the very end. That is the only verb whose tense determines the tense of the sentence.
That means that you should not really be calling 「使った」 the "past tense" only because there is a 「た」 in it. As I stated above, 「使った」 has no affect on the tense of the sentence.
Consider the English sentence (first of the two):
"I am eating a hamburger made with real Kobe beef. It's heavenly!"
The tense of the sentence itself is clearly the present progressive as the verb here is "am eating". If so, why use "made"? Is using "made" there incorrect?
I know very little English, but I still know that it is 100% correct, grammatical and natural to use "made" in that sentence. Or am I deluded?
Thus, 「使った」 is the most natural verb tense choice in the original sentence. 「使っている」 would sound quite awkward if not totally incorrect.