Temperament and behaviour have a strong genetic component, whilst socialisation and training are obviously extremely important neither can change what a dog is born with. This blog post on the subject (written by a veterinary behaviourist) is well worth a read.
If she's naturally rather anxious then she could also have been affected by the her very early care. The fact her litter was abandoned suggests they may not have received the appropriate care beforehand.
She sounds similar to our DDog2. She's naturally very sensitive and prone to anxiety, added to this she was taken away from her mum and litter mates far too young. She was our first puppy and we made mistakes with her which other dogs may have bounced right back from but had a very lasting effect on her. It took her a very long time to learn bite inhibition and also to grasp house training. She's got a tendency towards developing obsessive behaviours and has attachment issues, mostly surrounding DH. She is so ridiculously desperate to please that she's actually really hard to train because not being rewarded is like a terrible punishment for her.
She's extremely sensitive to our emotions and if either of us are in a bad mood she'll creep around as if she's expecting to be hit, despite the fact that in her nine years we've almost never so much as raised our voices at her. She's never been hit or physically reprimanded in any way at all but still sometimes acts like we're randomly going to beat her 
She does the food thing as well. I get up before DH so I feed all the dogs every morning. Her routine is that she'll stay upstairs with him until she hears me putting the bowls down. Most days she'll come belting down the stairs and burst into the kitchen all excited to have her breakfast and then randomly she'll come creeping down as if she's expecting disaster, poke her head in and retreat back upstairs without eating. Sometimes (like this morning) she'll come in, eat half and then suddenly slink off, though usually she will come back and finish with some gentle, happy encouragement.
She's got the added complication that her sight is pretty poor. She developed hereditary cataracts quite young and although she had surgery for them her sight is a long way from perfect. This means that if we catch her unawares sometimes she'll jump and cower.
Like yours, she's a completely different dog outside. She's supremely confident, great with people, dogs, other animals. She really is an absolutely rock solid, take anywhere dog outside.
She's so lovely but also very hard work sometimes. We love her to bits and whilst we don't regret getting her I'm not convinced it's been an experience we'd necessarily like to repeat!
I'd suggest nipping your girl to the vet just to check for anything physical which may be causing any problems, especially her sight and hearing. Then maybe look at getting a behaviourist in to help you support her as much as you can. If you go through one of these organisations you can be confident you're getting someone reputable.
It's also worth looking into calming products like Zylkene and Adaptil. There are also various supplements available which might be worth a try.
Does she have anywhere she go to which is completely away from everyone in the house? DDog2 really thrives when she's got the opportunity for plenty of alone time if she wants it.