It sounds like your DS has a milk allergy rather than an intolerance, but a non IgE mediated milk allergy so doesn't cause an immediate reaction. In the NICE guidelines for allergies (which you can find online) it clearly says allergies should be syspected with reflux symptoms that seem resistant to treatment, and same with eczema. Also very young babies very commonly have milk allergies. Most however also are allergic to soya.
If the eczema is bad, as in he has red patches and the hydromol stings, he needs to be prescribed steroid creams. Emollients like hydromol need to be applied frequency too, but they won't control a flare up. And every bodies skin is different with many emollients causing problems for people with eczema so they should give your DS a different one like epaderm for example.
He should really be prescribed neocate formula for this. It's a shame it's been left so late because it tasted disgusting and s lot of bobbies wont accept it after 4 months, but most are ok before 6 months.
Go to the nice guidelines for allergies, and go into the document for health professionals. Print it out and highlight the bits relevant to your DS (reflux, eczema and anything else) and take it to your GP. on page 7 it has the list of symptoms and in the non IgE column atopic eczema and reflux disease are listed. On page 8 it says about considering an allergy with these conditions.
On page 11 it says (under non-IgE mediated allergy '.. if non-IgE-mediated food allergy is suspected, trial elimination of the suspected allergen (normally for between 2?6 weeks) and reintroduce after the trial. Seek advice from a dietitian with appropriate competencies, about nutritional adequacies, timings of elimination and reintroduction, and follow-up.' and then on page 12 under 1.1.15 it sas they should prescribe a hypoallergenic formula. HTH :)