Your thinking on this is aligned with your feelings about the matter, but not in accordance with the facts. :-)
Think about it - what is the track number of these (actual) track names:
3 Minute Traffic Jam
1 2 3
2 Forms of Anger
2 Hillcrest
01 29
3.2 Bedrock
3:19 Intro
These track names begin with numbers. Which are correct? Hint: only 1 of 7 is correct.
MC did not eliminate the first two numbers. You did, by telling MC to rename the files according to a template.
The lack of field values is insufficient as a criteria for deciding not to use the template. There are perfectly valid, ordinary rules for writing out file names or file paths when certain fields are empty, such as Disc #. My templates use Disc # to specify the folder names, but most of the time Disc # is empty. So my rules must accommodate this.
It could be completely valid for a track name to have any combination of numbers in its name; that would be up to the artist. Without other info, such as Track# metadata field, MC should not make any assumptions.
Following is an actual example of what happened. This was iTunes ripped album, and therefore MC did not have the metadata.
This was the album before the MC Rename (taken from back-up drive):
01 Shine On You Crazy Diamond (Parts 1-5)
02 Welcome To The Machine
03 Have A Cigar
04 Wish You Were Here
05 Shine On You Crazy Diamond (Parts 6-9)
This was the album after the MC Rename:
00 - A Cigar
00 - On You Crazy Diamond (Parts (1)
00 - On You Crazy Diamond (Parts
00 - To The Machine
00 - You Were Here
Without Track# metadata, it would seem logical, that the following COULD have been the result, but was NOT:
00 - 01 Shine On You Crazy Diamond (Parts 1-5)
00 - 02 Welcome To The Machine
00 - 03 Have A Cigar
00 - 04 Wish You Were Here
00 - 05 Shine On You Crazy Diamond (Parts 6-9)
Before I ran the Rename on my entire library, I performed limited checking of how MC's Rename tool behaved, and I noticed that it did NOT double up the Track# on albums that already had that convention (but these were albums that were MC ripped), but on those albums the Rename operation was not performed. I erroneously assumed that would be the case with my iTunes ripped albums as well.
I am trying to provide constructive feedback to highlight how MC is operating counter-intuitive to a potential new user. It is important that a very complicated product behave intuitively. S/W developer need to look at their product with "new eyes", and not assume all users are intimately familiar with the products features and quirks.