Happee - if your bloods are always showing low estrogen, then you probably are not absorbing it well. It is important to separate the amount you are applying to your skin (whether gel or patches) from what you are actually getting into you (blood). Many people don't absorb well transdermally (myself included).
I was on gel only for a while and increased up to 12 pumps (!!!) trying to get my levels up, but on 12 pumps I was no higher than on 6 pumps - so I couldn't absorb more than that. I then added patches in as well. I am now on 300mcg of Estradot patches (3x 100mcg, where 100mcg is the max licensed dose) PLUS 4 pumps of gel. I was on 6 pumps, but I am gradually coming down on the gel and seeing what my levels are off it (and just on the 300mcg patches). I hate applying gel, waiting for it to dry and I worry about transfer to pets and partner, plus I am now bleeding too heavily during periods with flooding for 2 days. So I am reducing E. So far my symptoms are no worse and I've reduced by 2 pumps.
Anyways - that is all to say - you very likely need a lot MORE estrogen, especially if you have never tested with higher levels. You cannot rule out low estrogen as a cause of this, if you have never been able to trial higher levels in the blood. And taking a little bit of it but not enough, can upset homeostasis and cause more symptoms - which could be what happened when you started HRT.
If I were you, I would request a switch to Estradot patches (which are coming back into stock and IMO are the best patches) and then repeat tests privately if necessary to see if you can get levels up. If you reach 100mcg patches and still have low E, then you will need to go to a private menopause clinic to get prescribed higher off licence doses. As I do, with the Newson Clinic.