Good question, been wondering about this too. Following for an answer...

I think most pinmame Roms are padded to fill the entire "rom". It still shouldn't affect use in a real machine.

Correct

There is no difference between a pinmame romset and the real machine romset. The only thing done is add 00 bytes to the code to pad it to the full chip size. So if the game code is 1020 bytes, and the chip to be programmed is 1024 bytes, we add four bytes of 00 to fill out the rom space.
In a real machine it will work just the same as the original chip.

Well, sort of correct - the chips in the machines are already padded out with something - sometimes it's 00, sometimes it's $FF, sometimes it's random-y bytes. The self-test checksums in some machines will fail if you don't pad it out correctly.

It's 100% not an issue though if you read the original chips in, there's no padding needed. You've just read the data the manufacturer intended to have there so checksums will pass. (Checksum routines check the rom space size, not where the code ends)

For the OP, and as others have indicated, there's ZERO difference between "pinmame roms" and "real roms". The main reason you get pinmame sets is that they need to be named a certain way and formatted into the size pinmame expects.

Often when I need a romset I'll d/l the pinmame one because you can verify it in pinmame before burning.

Yup, as slochar says, naming is the main thing. The pinmame sets are properly named and setup for pinmame to read them. Meanwhile the other sets are often as they were released from the manufaturers, and sometimes include release notes, etc

My earthshaker has a PR-4 set of roms which turns out to be pinmame roms both pc and real machine there is no difference in game play the only difference is pinmame has a extra rom file u4-p1 for earthshaker and the files are slightly larger

That shouldn't be. Something's padded out that shouldn't be.

You should have a 256 and 128 rom for your main game chips. There shouldn't be slightly larger/smaller, it should be exactly 32768 (256) and 16384 (128) bytes.

I don't recall any pinmame rom files being "unpadded" or stripped of extra data. All the images I've seen are the standard chip sizes. Pinmame does support ZIP archives, it will extract the ROMS from a ZIP when needed, but that's about it.

When rom files are dumped sometime you can get a bad read.
If they are send to the ipdb they are added "as is".
No checking, no verification.
The Pinmame files are verified in Pinmame to be working correctly.

Be aware, the ipdb files may be old releases.
Better (other or older) versions are found all the time and added to Pinmame.
Not all those files get to be added to the ipdb.

I used to send files to the ipdb, but haven't done that in a VERY long time.
It is hard to keep the files up-to-date on the ipdb.
Their updates aren't regular and have long spaces in between.
That is why I stopped updating the ipdb Pinmame files.

The best place to fine the latest Pinmame files is at http://vpuniverse.com/forums/
All Pinmame files can be used in real games.

Peter