removing nextera transposase adapters, cutadapt
The adapter sequence you have googled is the sequence on the adapter primer. This works when you want to remove primer-dimers.

With transposase adapters or ATAC seq, you have very short fragments and you sequence into the adapter. So what you is sequenced is actually the reverse complement. See below image from trimmomatic manual



So if you look at what worked, and the sequence you googled, they are reverse complement of one another.

You can also see this in the NexteraPE-PE.fa, Trans1 and Trans1_rc @Haci recommended:

more NexteraPE-PE.fa 
&gt;PrefixNX/1
AGATGTGTATAAGAGACAG
&gt;PrefixNX/2
AGATGTGTATAAGAGACAG
&gt;Trans1
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
&gt;Trans1_rc
CTGTCTCTTATACACATCTGACGCTGCCGACGA
&gt;Trans2
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
&gt;Trans2_rc
CTGTCTCTTATACACATCTCCGAGCCCACGAGAC


To answer your question, if most of your fragments are short, and there's not a lot of primer dimers, then yes you are doing the right thing.