Before I came out I started with second hand shops because I didn't have a clue what size clothes I needed & didn't want to waste money on clothes that I may have had to have thrown out at a seconds notice.
Once I came out I had 2 female friends offer to take me clothes shopping for my birthday, after that I didn't care as much what people thought, if i'm in female mode then why the hell shouldn't I be buying womens clothes.
If I go in male mode then i'm not going to explain my actions, i've got just as much right to buy the clothes I like as any other person, i'm sure when I get to the counter they guess the situation as I never take my nail varnish off (& I love pink nail varnish).
No clothing shop assistants have ever given me a hard time, i've seen a few suppressed smirks but it's only ever a flicker, the majority are really polite & helpfull.
I have however left a few stores in a hurry due to hostile glances from other shoppers in the early days, the last time a shopper openly stared at me whilst in boy mode I grabbed the 2 most feminine tops within reach, held them up & asked which one she thought would look best on me.
If people try to make me feel awkward for being trans then I return the favour, if they are polite or helpfull then I try to return that courtesy