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Actually, this is more likely about the leftmost atom in the drawing rather than the first atom in the input (which does tend to end up on the left). Line ~645 in SvgWrapper.js:
// ... but for direction left move to the right to if(direction==='left'&&text[0][0]!==text[0][1]){bbox.width*=2.0;}
Atoms in the left direction get a double-width bounding box for some reason, and then this is used a little later to update the bounding box for the whole drawing, pushing things off center.
If the last atom in a SMILES string has a charge, the resulting molecule draws smaller and not quite centered:
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