I have a 20 year old hybrid that is fitted with a triple Sora FC-3303 crank in front, and a 9 speed Shimano MTB (Deore?) at rear. It has flat handlebar with thumb type shifters.

I am thinking to maybe change the front crankset. Today this is a square splinter and I would change to a Hollowtech II.b
I found the service instructions here:
https://si.shimano.com/pdfs/si/SI-1DP0A-000-00-ENG.pdf
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From this is seems that the bottom bracket is a BB-UN40 (113mm) with chain line 45mm, but when I measure it on the bike - it seems closer to 50mm (which is strange if the specified BB is used?). 50mm is more usual on MTB cranksets?

I am thinking of replacing it with a Sora FC-3505 triple crankset. I have ordered a FD-3505 front derailleur.

Some questions:
1. If the handlebar shifters work fine with the current setup, will it also work fine with the Sora FC-3503? I understand that it might be a bit strange with flag handlebar shifters for a road crankset - but it works fine today.
2. What about the chainline? The specification for the FC-3505 says 45mm, but I measure closer to 50mm on the bike - will this be any issue? What does the chainline affect? Is it just the space between frame and cogs? Or can there be issues with the shifters or adjusting derailleur correctly as well?
3. Since this is flat handlebar - would it make more sense to rebuild to a MTB front crank and shifters instead? There are a lot more flat handlebar shifters to choose from. I see that chainline on these are 50mm - which fits with what I have today.