Couple things are wrong with this.
1. If Spike is part-pony then Celestia would have to be male since ponies do live births and do not lay eggs.
Strictly speaking, most half-breeds in fiction are physically impossible, but the fantasy genre is littered with them. Ponies are basically a replacement for humans in MLP, and human/dragon hybrids are very common. Once you get past the fact that it's physically impossible in our world, there can be various new rules introduced that make it possible in fictional ones. I know I've seen (fictional) examples of human women laying eggs. Often times "a wizard" makes such things possible, and Celestia wouldn't have to look far to find a wizard since she's already one of the best in her universe.
Then you would have to explain the lack of wings and any other pony trait in the offspring of a pony god.
We don't know if pony genetics work the way we think they should (something the show already teased us about), and we know next to nothing about dragons, and even less about what the rules are regarding pony/dragon hybrids, if they exist.
I will admit she did something to him after he was born in giving him magic fire and stunted his growth which explains the size change in Secrets of My Excess when greedy Spike goes through puberty and hits adulthood when he's greedy and why he's smaller than all of the 'teen' dragons.
No reason to assume that Celestia "did those things" to Spike. Those could be dragon traits for all we know.
It's possible that normally any dragon can transport anything combustible to any other dragon, but that a dragon once taught Celestia to produce dragonfire (and then they slept together, but the dragon was a dick so he never wrote her any letters like he promised). In a related note, it's possible that Celestia is ageless not because she's an Alicorn, but because Philomeena taught Celestia how to produce phoenix fire.
War orphan is just a more believable back-story than genetic offspring of a pony god & a dragon.
More believable to you. Any theories that fits the facts (and some that don't) are valid until the writers show their cards. It never occurred to me before this episode that Spike could by a hybrid, and I think that simplifies his backstory (it means there's no need to look farther than Celestia). It potentially answers some questions, while raising many more, which elevates this episode, where some people have complained because they expected to get more info about Spike but found nothing.