You've done a far, far better job than the paid professional did. Nobody will sit in there wondering how long it took you; they'll just see how good/bad a job has been done.
For putting silicone around the toilet base, I used the Fugi kit (Google Fugi silicone kit). I used to use masking tape which I peeled off to get a clean line, but this makes it a lot easier and will work well around the base. Good for doing around the bath as well.
Tiling in first pic was not planned correctly, you avoid any small cuts and plan tiles accordingly.
He basically said he'd go bankrupt if he spent time doing perfect cuts
Depending on how flexible it is you may be able to pull the panel forward slightly and pack behind the screws. If the panel sits behind very thick tiles it may be tricky though.
I tend to tile under the panel and then refit so there is a clean edge.
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