David – I do a lot of comparing of texts and mostly don't have the Compare box checked. The window I use for my daily reading always has at least two English versions open in parallel in each tab. I always have the NAS95 as my search text. When I run into differences and want to see what a bunch of versions say, I will amplify to a custom window that has 16 texts. I use the NAS95 as my search text there, too. This screen shot may be hard to make out unless you blow it up, but you'll able to see the set-up.
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Each translation team has to decide what to do with the phrases/verses that are not found in the NA28th (or whichever modern Greek text they're working from). The NASB/NAS95 team decided to include the extra stuff within the text and just put it it brackets w/footnote to let the reader know that the textual support for the phrase/verse is poor. If one is sitting in a group and the teacher or preacher has a KJV or NKJV in front of him, the NAS95 reader is looking at a similar text. The ESV/NRSV/NIV reader will be seeing a couple of dashes and some extra space but will find the text in his footnotes.
The ESV committee (and many others) decided to put the poorly supported words/verses in the footnotes. Frankly, I wish the NASB/NAS95 had done the same. I have marked the poorly supported parts of the English text in the versions I most often use.
Since I have become aware of the differing approaches of the various committees, using the NAS95 as my search text avoids the issues you have been running into. Accordance functioning the way it does has not caused any difficulties for me. I find using the Compare box is much more useful when I'm examining closely related texts: KJV & NKJV, NASB & NAS95, GNT28-T and GNT-TR. Using Compare with the NIV and KJV doesn't give me much help.
That said, it would be helpful if, when starting with one of the texts that takes the ESV/NRSV approach to poorly supported readings, the words would still be displayed in the NAS95, NKJV & others, or that there would at least be an indication that the text differed.