I guess that some things have changed since MAME 0.108. I normally don't use anything older than 0.119 and a lot of what you're questioning is what I would accept as normal. I'll try and answer to the best of my knowledge but keep in mind, some stuff may not apply to an older MAME like 0.108.
Q1. So , can I alter all the settings of neogeo games like time , difficulty etc in the menu that come up by pressing f2 ?
Yes, I think so. That's how I do it in all the newer MAMEs I use.
Q2. Is it completely same as using mameplus" tab-dipswitch menu ?
I've never heard of the Neo Geo dipswitch method you described before. I'd say that at some point, for the sake of accuracy, the MAME Devs moved most of the Neo Geo dipswitch stuff into the F2 service menu instead, just as it would be on a real Neo Geo. In my experience of newer MAME, the tab menu dipswitches for Neo Geo games are identical between MAMEPlus! and MAMEUIFX and are very limited in their usefulness (see screen below). Most of the needed options for each game are in the F2 service menu instead.
Q3. Can I get the in-game menu where I could select versus team , versus 1p , practice , ... ?
That is a complicated area. I may have to revise what I said in my previous post about the AES part of the bios not being recognised in MAMEUIFX. I have something like a super neogeo.zip file that I constructed myself from various bits and pieces I searched and added. I'm using this one Neo Geo bios for all my MAMEs. I did this around the time of 0.134, which is when I first got into normal MAMEPlus! (as opposed to MAME32 Plus! Plus! 0.119 for Kaillera).
Prior to that I had mainly been using MAMEUIFX 0.128 and 0.132 for offline play. Since they're both older than 0.134, it's possible that some parts of my bios are not compatible with those versions of MAMEUIFX. For example, none of the Universe bios's show in MAMEUIFX 0.128, while they do show in 0.132 (as in my neodrvr.c Properties screenshot in previous post). Now, in MAMEPlus! 0.134 I also have the Asia AES and Japan AES bios's available. Now that I think on it, it seems more likely that MAME/bios version compatibility is the issue for me. I'd say that MAMEUIFX should be capable of recognising a compatible AES bios.
In any case, even though I don't get the standard AES bios's showing up in my MAMEUIFXs, so long as the Universe bios is available it's still possible to set it to AES for things like Practice Mode in KOF'98.
Q4. Does it have any disadvantage compared to mameplus" tab-dipsw method ?
Again, I don't know since the MAME tab menu Neo Geo dipswitch options for both MAMEPlus! and MAMEUIFX are identical for all the versions I'm using (as in the screen for Q2. above). So, there are no effective advantages/disadvantages with those dipswitches for me and it doesn't matter anyway since the needed options are in the F2 service menu instead.
Q5. I wonder my old mameplus didnt show the green screens btw...
I'm guessing that it's because you always play in AES mode. The green boot up screen is perfectly normal for MVS mode though.
Q6. Finally , can you please teach how did you get to the settings menu you posted here :
I had some trouble navigating the neogeo games" f2 menu which I entered first time
Sure can. My "How To Turn Blood ON In Metal Slug"
video actually has a quick demonstration of the Neo Geo service menu.